Title: Thermal Image Analysis
Description: A collection of functions and routines for inputting thermal
image video files, plotting and converting binary raw data into estimates of
temperature. First published 2015-03-26. Written primarily for research purposes
in biological applications of thermal images. v1 included the base calculations
for converting thermal image binary values to temperatures. v2 included additional
equations for providing heat transfer calculations and an import function for thermal
image files (v2.2.3 fixed error importing thermal image to windows OS). v3. Added numerous
functions for converting thermal image, videos, rewriting and exporting.
v3.1. Added new functions to convert files.
Author: Glenn J. Tattersall
Maintainer: Glenn J. Tattersall <gtatters@brocku.ca>
Diff between Thermimage versions 3.0.0 dated 2017-03-25 and 3.1.0 dated 2017-11-29
Thermimage-3.0.0/Thermimage/README.md |only Thermimage-3.1.0/Thermimage/DESCRIPTION | 18 ++++--- Thermimage-3.1.0/Thermimage/MD5 | 41 ++++++++++------- Thermimage-3.1.0/Thermimage/NAMESPACE | 3 + Thermimage-3.1.0/Thermimage/R/convertflirJPG.R |only Thermimage-3.1.0/Thermimage/R/convertflirVID.R |only Thermimage-3.1.0/Thermimage/R/ffmpegcall.R |only Thermimage-3.1.0/Thermimage/R/flirsettings.R | 12 ++-- Thermimage-3.1.0/Thermimage/R/frameLocates.R | 8 +-- Thermimage-3.1.0/Thermimage/R/getFrames.R | 13 ++++- Thermimage-3.1.0/Thermimage/R/hconv.R | 8 ++- Thermimage-3.1.0/Thermimage/R/locate.fid.R | 4 - Thermimage-3.1.0/Thermimage/R/readflirJPG.R | 4 + Thermimage-3.1.0/Thermimage/data/rainbow1234pal.RData |only Thermimage-3.1.0/Thermimage/inst/extdata/SampleCSQ.csq |only Thermimage-3.1.0/Thermimage/inst/perl |only Thermimage-3.1.0/Thermimage/man/convertflirJPG.Rd |only Thermimage-3.1.0/Thermimage/man/convertflirVID.Rd |only Thermimage-3.1.0/Thermimage/man/ffmpegcall.Rd |only Thermimage-3.1.0/Thermimage/man/getFrames.Rd | 16 ++++-- Thermimage-3.1.0/Thermimage/man/hconv.Rd | 6 +- Thermimage-3.1.0/Thermimage/man/qconv.Rd | 16 +++--- Thermimage-3.1.0/Thermimage/man/rainbow1234pal.Rd |only Thermimage-3.1.0/Thermimage/man/readflirJPG.Rd | 10 +++- Thermimage-3.1.0/Thermimage/man/thermsumcent.Rd | 2 Thermimage-3.1.0/Thermimage/man/writeFlirBin.Rd | 5 +- 26 files changed, 109 insertions(+), 57 deletions(-)
Title: Observatory of Economic Complexity API Wrapper and Utility
Program
Description: Access The Observatory of Economic Complexity API from R to download international trade data and create and D3Plus visualizations.
Author: Mauricio Vargas S. [aut, cre],
Cesar Hidalgo [aut] (original OEC idea),
Alexander Simoes [aut] (original OEC idea),
Manuel Aristaran [ctb],
Pablo Paladino [ctb],
Gabriela Perez [ctb],
Dave Landry [ctb] (D3plus author),
Mike Bostock [ctb] (D3 author),
UN Comtrade [dtc],
MIT Media Lab [dtc],
Datawheel [fnd, cph]
Maintainer: Mauricio Vargas S. <oec@media.mit.edu>
Diff between oec versions 2.5 dated 2017-11-01 and 2.5.2 dated 2017-11-29
DESCRIPTION | 47 ++++++++++----- MD5 | 19 ++++-- NAMESPACE | 12 +++- R/getdata.R | 128 ++++++++++++++++++++++++++++++++++--------- build |only data/countries_list.RData |binary data/hs92.RData |binary data/sitc.RData |binary inst/doc |only inst/extdata/demo_examples.R | 4 + vignettes |only 11 files changed, 161 insertions(+), 49 deletions(-)
Title: A Modular Platform for Reproducible Modeling of Species Niches
and Distributions
Description: The 'shiny' application 'wallace' is a modular platform for reproducible modeling of species niches and distributions. 'wallace' guides users through a complete analysis, from the acquisition of species occurrence and environmental data to visualizing model predictions on an interactive map, thus bundling complex workflows into a single, streamlined interface.
Author: Jamie M. Kass [aut, cre],
Bruno Vilela [aut],
Matthew E. Aiello-Lammens [aut],
Robert Muscarella [aut],
Cory Merow [aut],
Robert P. Anderson [aut]
Maintainer: Jamie M. Kass <jkass@gradcenter.cuny.edu>
Diff between wallace versions 1.0 dated 2017-11-25 and 1.0.1 dated 2017-11-29
wallace-1.0.1/wallace/DESCRIPTION | 16 ++++++++-------- wallace-1.0.1/wallace/MD5 | 20 ++++++++++---------- wallace-1.0.1/wallace/NEWS.md | 6 +++++- wallace-1.0.1/wallace/R/run_wallace.R | 2 +- wallace-1.0.1/wallace/R/wallace-package.R | 6 +++--- wallace-1.0.1/wallace/README.md | 2 +- wallace-1.0.1/wallace/inst/Rmd/text_intro.Rmd | 2 +- wallace-1.0.1/wallace/inst/Rmd/text_intro_tab.Rmd | 2 +- wallace-1.0.1/wallace/inst/shiny/ui.R | 2 +- wallace-1.0.1/wallace/man/wallace-package.Rd | 7 ++++--- wallace-1.0.1/wallace/tests/README.txt |only wallace-1.0/wallace/tests/README.rtf |only 12 files changed, 35 insertions(+), 30 deletions(-)
Title: Ranking of Pathogen Strains
Description: Regression-based ranking of pathogen strains with respect to their contributions to natural epidemics, using demographic and genetic data sampled in the curse of the epidemics. This package also includes the GMCPIC test.
Author: Soubeyrand, S., Tollenaere, C., Haon-Lasportes, E. and Laine, A.-L.
Maintainer: Samuel Soubeyrand <samuel.soubeyrand@inra.fr>
Diff between StrainRanking versions 1.1 dated 2014-02-05 and 1.2 dated 2017-11-29
DESCRIPTION | 20 +++--- LICENSE |only MD5 | 31 ++++++++-- NAMESPACE | 4 - R/functions.R | 71 ++++++++++------------- R/functions2.R |only R/rankingStrains.R | 22 +++---- data/PathogenCompositionMoryzaeChina.rda |only data/PathogenCompositionMoryzaeMadagascar.rda |only data/PathogenCompositionPsyringaeClades.rda |only data/PathogenCompositionPsyringaeHaplotypes.rda |only data/PathogenCompositionPsyringaePhylogroups.rda |only data/PathogenCompositionPtriticinaGalibier.rda |only data/PathogenCompositionPtriticinaKalango.rda |only man/PathogenCompositionMoryzaeChina.Rd |only man/PathogenCompositionMoryzaeMadagascar.Rd |only man/PathogenCompositionPsyringaeClades.Rd |only man/PathogenCompositionPsyringaeHaplotypes.Rd |only man/PathogenCompositionPsyringaePhylogroups.Rd |only man/PathogenCompositionPtriticinaGalibier.Rd |only man/PathogenCompositionPtriticinaKalango.Rd |only man/StrainRanking-package.Rd | 33 ++-------- man/gmcpic.test.Rd |only man/ranking.strains.Rd | 16 +++-- src |only 25 files changed, 101 insertions(+), 96 deletions(-)
Title: Tools for Combinatorics and Computational Mathematics
Description: Provides optimized functions implemented in C++ with 'Rcpp'
for solving problems in combinatorics and computational mathematics.
There is a combination function and a permutation function that are
both flexible as well as efficient with respect to speed and memory.
There are optional contraint arguments that when employed, generate
all combinations/permutations of a vector meeting a specific criteria
(E.g. finding all combinations such that the sum is less than a
bound). The generalized permutation function is also capable of
producing all permutations of multisets. Additionally, there are
various sieving functions that quickly generate essential components
for problems common in computational mathematics (E.g. number of
comprime elements, divisors, prime factorizations, and complete
factorizations for many numbers as well as primes in a range).
Author: Joseph Wood
Maintainer: Joseph Wood <jwood000@gmail.com>
Diff between RcppAlgos versions 0.2.0 dated 2017-11-28 and 0.2.1 dated 2017-11-29
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/Combinatorics.R | 2 +- man/primeSieve.Rd | 10 +++++++--- src/CombinatoricsContainer.cpp | 30 +++++++++++++++++++----------- 5 files changed, 34 insertions(+), 22 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polytomous response data using
unidimensional and multidimensional latent trait models under the Item
Response Theory paradigm (Chalmers (2012) <doi:10.18637/jss.v048.i06>).
Exploratory and confirmatory models can be estimated with quadrature (EM)
or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier analyses are available for modeling item testlets.
Multiple group analysis and mixed effects designs also are available for
detecting differential item and test functioning as well as modelling
item and person covariates. Finally, latent class models such as the DINA,
DINO, multidimensional latent class, and several other discrete latent
variable models are supported.
Author: Phil Chalmers [aut, cre, cph],
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb],
KwonHyun Kim [ctb],
Carl F. Falk [ctb],
Adam Meade [ctb],
Lennart Schneider [ctb],
David King [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.26.1 dated 2017-11-27 and 1.26.3 dated 2017-11-29
DESCRIPTION | 11 +- MD5 | 62 +++++------ NEWS.md | 5 R/SIBTEST.R | 1 R/areainfo.R | 2 R/createGroup.R | 3 R/expand.table.R | 3 R/expected.item.R | 2 R/fscores.R | 4 R/iteminfo.R | 3 R/marginal_rxx.R | 3 R/mdirt.R | 3 R/mirt.R | 6 - R/probtrace.R | 3 R/simdata.R | 3 R/testinfo.R | 3 build/partial.rdb |binary man/SIBTEST.Rd | 1 man/areainfo.Rd | 2 man/createGroup.Rd | 3 man/expand.table.Rd | 3 man/expected.item.Rd | 2 man/fscores.Rd | 4 man/iteminfo.Rd | 3 man/marginal_rxx.Rd | 3 man/mdirt.Rd | 2 man/mirt.Rd | 6 - man/probtrace.Rd | 3 man/simdata.Rd | 3 man/testinfo.Rd | 3 src/dpars.cpp | 7 - src/ggum_derivs.cpp | 280 +++++++++++++++++++++++++-------------------------- 32 files changed, 222 insertions(+), 220 deletions(-)
Title: Learning Interactions via Hierarchical Group-Lasso
Regularization
Description: Group-Lasso INTERaction-NET. Fits linear pairwise-interaction models that satisfy strong hierarchy: if an interaction coefficient is estimated to be nonzero, then its two associated main effects also have nonzero estimated coefficients. Accommodates categorical variables (factors) with arbitrary numbers of levels, continuous variables, and combinations thereof. Implements the machinery described in the paper "Learning interactions via hierarchical group-lasso regularization" (JCGS 2015, Volume 24, Issue 3). Michael Lim & Trevor Hastie (2015) <DOI:10.1080/10618600.2014.938812>.
Author: Michael Lim, Trevor Hastie
Maintainer: Michael Lim <michael626@gmail.com>
Diff between glinternet versions 1.0.5 dated 2017-07-08 and 1.0.6 dated 2017-11-29
DESCRIPTION | 8 ++-- MD5 | 6 +-- R/glinternet.cv.r | 59 ++++++++++++++++++++--------------- R/glinternet.r | 89 ++++++++++++++++++++++++++++-------------------------- 4 files changed, 88 insertions(+), 74 deletions(-)
Title: C-Like 'getopt' Behavior
Description: Package designed to be used with Rscript to write
``#!'' shebang scripts that accept short and long flags/options.
Many users will prefer using instead the packages optparse or argparse
which add extra features like automatically generated help option and usage,
support for default values, positional argument support, etc.
Author: Allen Day.
Contributions from Trevor L Davis and Roman Zenka.
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between getopt versions 1.20.0 dated 2013-08-30 and 1.20.1 dated 2017-11-29
getopt-1.20.0/getopt/inst |only getopt-1.20.1/getopt/DESCRIPTION | 15 - getopt-1.20.1/getopt/MD5 | 19 - getopt-1.20.1/getopt/NAMESPACE | 3 getopt-1.20.1/getopt/NEWS | 9 getopt-1.20.1/getopt/R/getopt.R | 244 +++++++++--------- getopt-1.20.1/getopt/exec |only getopt-1.20.1/getopt/man/get_Rscript_filename.Rd | 12 getopt-1.20.1/getopt/man/getopt.Rd | 311 ++++++++++------------- getopt-1.20.1/getopt/man/sort_list.Rd | 11 getopt-1.20.1/getopt/tests/run-all.R | 3 getopt-1.20.1/getopt/tests/testthat |only 12 files changed, 310 insertions(+), 317 deletions(-)
Title: R Markdown Format for Flexible Dashboards
Description: Format for converting an R Markdown document to a grid oriented
dashboard. The dashboard flexibly adapts the size of it's components to the
containing web page.
Author: Barbara Borges [aut, cre],
JJ Allaire [aut],
RStudio [cph],
Keen IO [ctb, cph] (Dashboard CSS),
Abdullah Almsaeed [ctb, cph] (Dashboard CSS),
Jonas Mosbech [ctb, cph] (StickyTableHeaders),
Noel Bossart [ctb, cph] (Featherlight),
Lea Verou [ctb, cph] (Prism),
Dmitry Baranovskiy [ctb, cph] (Raphael.js),
Sencha Labs [ctb, cph] (Raphael.js),
Bojan Djuricic [ctb, cph] (JustGage),
Tomas Sardyha [ctb, cph] (Sly),
Bryan Lewis [ctb, cph] (Examples),
Carson Sievert [ctb, cph] (Examples),
Joshua Kunst [ctb, cph] (Examples),
Ryan Hafen [ctb, cph] (Examples),
Bob Rudis [ctb, cph] (Examples),
Joe Cheng [ctb] (Examples)
Maintainer: Barbara Borges <barbara@rstudio.com>
Diff between flexdashboard versions 0.5 dated 2017-03-13 and 0.5.1 dated 2017-11-29
flexdashboard-0.5.1/flexdashboard/DESCRIPTION | 14 ++++--- flexdashboard-0.5.1/flexdashboard/MD5 | 20 ++-------- flexdashboard-0.5.1/flexdashboard/NEWS.md |only flexdashboard-0.5.1/flexdashboard/R/flex_dashboard.R | 5 +- flexdashboard-0.5.1/flexdashboard/inst/rmarkdown/templates/flex_dashboard/resources/flexdashboard.js | 3 + flexdashboard-0.5.1/flexdashboard/man/flex_dashboard.Rd | 8 ++-- flexdashboard-0.5/flexdashboard/inst/NEWS |only flexdashboard-0.5/flexdashboard/inst/examples/shiny-biclust_data |only flexdashboard-0.5/flexdashboard/inst/examples/shiny-eruptions_data |only flexdashboard-0.5/flexdashboard/inst/examples/shiny-ggplot2-brushing_data |only flexdashboard-0.5/flexdashboard/inst/examples/shiny-ggplot2-diamonds_data |only flexdashboard-0.5/flexdashboard/inst/examples/shiny-kmeans_data |only 12 files changed, 22 insertions(+), 28 deletions(-)
Title: Agricultural Datasets
Description: Datasets from books, papers, and websites related to agriculture.
Example graphics and analyses are included. Data come from small-plot trials,
multi-environment trials, uniformity trials, yield monitors, and more.
Author: Kevin Wright [aut, cre]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between agridat versions 1.12 dated 2015-06-29 and 1.13 dated 2017-11-29
agridat-1.12/agridat/NEWS |only agridat-1.12/agridat/R |only agridat-1.12/agridat/README |only agridat-1.12/agridat/README.md |only agridat-1.12/agridat/data/aastveit.barley.rda |only agridat-1.12/agridat/data/ortiz.tomato.rda |only agridat-1.12/agridat/data/steel.soybean.txt.gz |only agridat-1.12/agridat/data/talbot.potato.rda |only agridat-1.12/agridat/data/vargas.txe.rda |only agridat-1.12/agridat/data/vargas.wheat1.rda |only agridat-1.12/agridat/data/vargas.wheat2.rda |only agridat-1.12/agridat/data/wassom.brome1.uniformity.txt.gz |only agridat-1.12/agridat/data/wassom.brome2.uniformity.txt.gz |only agridat-1.12/agridat/data/wassom.brome3.uniformity.txt.gz |only agridat-1.12/agridat/inst/doc/agridat_examples.Rnw |only agridat-1.12/agridat/inst/files/theobald.bug |only agridat-1.12/agridat/man/RedGrayBlue.Rd |only agridat-1.12/agridat/man/bridges.cucmber.Rd |only agridat-1.12/agridat/man/desplot.Rd |only agridat-1.12/agridat/man/figures |only agridat-1.12/agridat/man/garber.mulit.uniformity.Rd |only agridat-1.12/agridat/man/gge.Rd |only agridat-1.12/agridat/man/panel.outlinelevelplot.Rd |only agridat-1.12/agridat/man/steel.soybean.Rd |only agridat-1.12/agridat/man/wassom.brome1.uniformity.Rd |only agridat-1.12/agridat/vignettes/agridat-concordance.tex |only agridat-1.12/agridat/vignettes/agridat_examples.Rnw |only agridat-1.13/agridat/DESCRIPTION | 32 agridat-1.13/agridat/LICENSE.note |only agridat-1.13/agridat/MD5 | 839 +++++----- agridat-1.13/agridat/NAMESPACE | 21 agridat-1.13/agridat/build/vignette.rds |binary agridat-1.13/agridat/data/aastveit.barley.covs.txt.gz |only agridat-1.13/agridat/data/aastveit.barley.height.txt.gz |only agridat-1.13/agridat/data/acorsi.grayleafspot.txt.gz |only agridat-1.13/agridat/data/adugna.sorghum.txt.gz |binary agridat-1.13/agridat/data/ars.earlywhitecorn96.txt.gz |binary agridat-1.13/agridat/data/baker.barley.uniformity.txt.gz |binary agridat-1.13/agridat/data/battese.survey.txt.gz |only agridat-1.13/agridat/data/beall.webworms.txt.gz |binary agridat-1.13/agridat/data/beaven.barley.txt.gz |binary agridat-1.13/agridat/data/becker.chicken.txt.gz |only agridat-1.13/agridat/data/besag.beans.txt.gz |binary agridat-1.13/agridat/data/besag.elbatan.txt.gz |binary agridat-1.13/agridat/data/besag.endive.txt.gz |binary agridat-1.13/agridat/data/besag.triticale.txt.gz |binary agridat-1.13/agridat/data/bliss.borers.txt.gz |binary agridat-1.13/agridat/data/box.cork.txt.gz |binary agridat-1.13/agridat/data/bradley.multi.uniformity.txt.gz |only agridat-1.13/agridat/data/brandle.rape.txt.gz |binary agridat-1.13/agridat/data/brandt.switchback.txt.gz |binary agridat-1.13/agridat/data/burgueno.alpha.txt.gz |binary agridat-1.13/agridat/data/burgueno.rowcol.txt.gz |binary agridat-1.13/agridat/data/burgueno.unreplicated.txt.gz |binary agridat-1.13/agridat/data/butron.maize.txt.gz |binary agridat-1.13/agridat/data/byers.apple.txt.gz |binary agridat-1.13/agridat/data/carlson.germination.txt.gz 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agridat-1.13/agridat/data/harris.multi.uniformity.txt.gz |binary agridat-1.13/agridat/data/harris.wateruse.txt.gz |binary agridat-1.13/agridat/data/harrison.priors.txt.gz |binary agridat-1.13/agridat/data/harvey.lsmeans.txt.gz |only agridat-1.13/agridat/data/harville.lamb.txt.gz |only agridat-1.13/agridat/data/hayman.tobacco.txt.gz |binary agridat-1.13/agridat/data/hazell.vegetables.txt.gz |binary agridat-1.13/agridat/data/heady.fertilizer.txt.gz |binary agridat-1.13/agridat/data/henderson.milkfat.txt.gz |binary agridat-1.13/agridat/data/hernandez.nitrogen.txt.gz |binary agridat-1.13/agridat/data/holland.arthropods.txt.gz |binary agridat-1.13/agridat/data/holshouser.splitstrip.txt.gz |binary agridat-1.13/agridat/data/holtsmark.timothy.uniformity.txt.gz |only agridat-1.13/agridat/data/huehn.wheat.txt.gz |only agridat-1.13/agridat/data/hunter.corn.txt.gz |binary agridat-1.13/agridat/data/immer.sugarbeet.uniformity.txt.gz |binary agridat-1.13/agridat/data/ivins.herbs.txt.gz |binary 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agridat-1.13/agridat/man/hanks.sprinkler.Rd | 114 - agridat-1.13/agridat/man/hanover.whitepine.Rd |only agridat-1.13/agridat/man/harris.multi.uniformity.Rd | 65 agridat-1.13/agridat/man/harris.wateruse.Rd | 13 agridat-1.13/agridat/man/harrison.priors.Rd | 2 agridat-1.13/agridat/man/harvey.lsmeans.Rd |only agridat-1.13/agridat/man/harville.lamb.Rd |only agridat-1.13/agridat/man/hayman.tobacco.Rd | 24 agridat-1.13/agridat/man/hazell.vegetables.Rd | 137 + agridat-1.13/agridat/man/heady.fertilizer.Rd | 19 agridat-1.13/agridat/man/henderson.milkfat.Rd | 4 agridat-1.13/agridat/man/hernandez.nitrogen.Rd | 26 agridat-1.13/agridat/man/hessling.argentina.Rd | 34 agridat-1.13/agridat/man/hildebrand.systems.Rd | 141 + agridat-1.13/agridat/man/holland.arthropods.Rd | 38 agridat-1.13/agridat/man/holshouser.splitstrip.Rd | 61 agridat-1.13/agridat/man/holtsmark.timothy.uniformity.Rd |only agridat-1.13/agridat/man/huehn.wheat.Rd |only agridat-1.13/agridat/man/hughes.grapes.Rd | 62 agridat-1.13/agridat/man/hunter.corn.Rd | 7 agridat-1.13/agridat/man/ilri.sheep.Rd | 109 - agridat-1.13/agridat/man/immer.sugarbeet.uniformity.Rd | 46 agridat-1.13/agridat/man/ivins.herbs.Rd | 17 agridat-1.13/agridat/man/iyer.wheat.uniformity.Rd |only agridat-1.13/agridat/man/jansen.apple.Rd | 9 agridat-1.13/agridat/man/jansen.carrot.Rd | 15 agridat-1.13/agridat/man/jansen.strawberry.Rd | 45 agridat-1.13/agridat/man/jenkyn.mildew.Rd | 5 agridat-1.13/agridat/man/john.alpha.Rd | 159 + agridat-1.13/agridat/man/johnson.blight.Rd | 18 agridat-1.13/agridat/man/kadam.millet.uniformity.Rd |only agridat-1.13/agridat/man/kalamkar.potato.uniformity.Rd | 23 agridat-1.13/agridat/man/kalamkar.wheat.uniformity.Rd |only agridat-1.13/agridat/man/kang.maize.Rd | 16 agridat-1.13/agridat/man/kang.peanut.Rd | 15 agridat-1.13/agridat/man/karcher.turfgrass.Rd | 1 agridat-1.13/agridat/man/keen.potatodamage.Rd | 8 agridat-1.13/agridat/man/kempton.barley.uniformity.Rd | 88 - agridat-1.13/agridat/man/kempton.competition.Rd | 12 agridat-1.13/agridat/man/kempton.rowcol.Rd | 40 agridat-1.13/agridat/man/kempton.slatehall.Rd | 110 - agridat-1.13/agridat/man/kenward.cattle.Rd |only agridat-1.13/agridat/man/khin.rice.uniformity.Rd |only agridat-1.13/agridat/man/kiesselbach.oats.uniformity.Rd |only agridat-1.13/agridat/man/kreusler.maize.Rd |only agridat-1.13/agridat/man/kristensen.barley.uniformity.Rd |only agridat-1.13/agridat/man/lambert.soiltemp.Rd | 12 agridat-1.13/agridat/man/lasrosas.corn.Rd | 23 agridat-1.13/agridat/man/lavoranti.eucalyptus.Rd | 19 agridat-1.13/agridat/man/lee.potatoblight.Rd | 37 agridat-1.13/agridat/man/lehner.soybeanmold.Rd |only agridat-1.13/agridat/man/lessman.sorghum.uniformity.Rd |only agridat-1.13/agridat/man/li.millet.uniformity.Rd | 28 agridat-1.13/agridat/man/lillemo.wheat.Rd |only agridat-1.13/agridat/man/lin.superiority.Rd |only agridat-1.13/agridat/man/lin.unbalanced.Rd |only agridat-1.13/agridat/man/little.splitblock.Rd |only agridat-1.13/agridat/man/lonnquist.maize.Rd | 94 - agridat-1.13/agridat/man/love.cotton.uniformity.Rd |only agridat-1.13/agridat/man/lu.stability.Rd |only agridat-1.13/agridat/man/lucas.switchback.Rd | 33 agridat-1.13/agridat/man/lyon.potato.uniformity.Rd | 46 agridat-1.13/agridat/man/lyons.wheat.Rd | 5 agridat-1.13/agridat/man/masood.rice.uniformity.Rd |only agridat-1.13/agridat/man/mcclelland.corn.uniformity.Rd |only agridat-1.13/agridat/man/mcconway.turnip.Rd | 15 agridat-1.13/agridat/man/mcleod.barley.Rd | 16 agridat-1.13/agridat/man/mead.cauliflower.Rd | 9 agridat-1.13/agridat/man/mead.cowpeamaize.Rd | 20 agridat-1.13/agridat/man/mead.germination.Rd | 12 agridat-1.13/agridat/man/mead.lamb.Rd |only agridat-1.13/agridat/man/mead.strawberry.Rd | 21 agridat-1.13/agridat/man/mercer.mangold.uniformity.Rd | 46 agridat-1.13/agridat/man/mercer.wheat.uniformity.Rd | 101 - agridat-1.13/agridat/man/minnesota.barley.weather.Rd | 39 agridat-1.13/agridat/man/minnesota.barley.yield.Rd | 18 agridat-1.13/agridat/man/montgomery.wheat.uniformity.Rd |only agridat-1.13/agridat/man/moore.uniformity.Rd |only agridat-1.13/agridat/man/nass.corn.Rd | 14 agridat-1.13/agridat/man/nebraska.farmincome.Rd | 27 agridat-1.13/agridat/man/nonnecke.corn.uniformity.Rd |only agridat-1.13/agridat/man/nonnecke.peas.uniformity.Rd |only agridat-1.13/agridat/man/odland.soy.uniformity.Rd | 61 agridat-1.13/agridat/man/omer.sorghum.Rd |only agridat-1.13/agridat/man/onofri.winterwheat.Rd |only agridat-1.13/agridat/man/ortiz.tomato.Rd | 121 - agridat-1.13/agridat/man/pacheco.soybean.Rd | 9 agridat-1.13/agridat/man/parker.orange.uniformity.Rd |only agridat-1.13/agridat/man/patterson.switchback.Rd | 40 agridat-1.13/agridat/man/pearce.apple.Rd | 10 agridat-1.13/agridat/man/pearl.kernels.Rd | 15 agridat-1.13/agridat/man/perry.springwheat.Rd | 50 agridat-1.13/agridat/man/piepho.cocksfoot.Rd | 7 agridat-1.13/agridat/man/polson.safflower.uniformity.Rd |only agridat-1.13/agridat/man/ratkowsky.onions.Rd | 8 agridat-1.13/agridat/man/reid.grasses.Rd |only agridat-1.13/agridat/man/ridout.appleshoots.Rd | 25 agridat-1.13/agridat/man/rothamsted.brussels.Rd | 23 agridat-1.13/agridat/man/ryder.groundnut.Rd | 38 agridat-1.13/agridat/man/salmon.bunt.Rd | 10 agridat-1.13/agridat/man/sawyer.multi.uniformity.Rd |only agridat-1.13/agridat/man/senshu.rice.Rd | 23 agridat-1.13/agridat/man/shafii.rapeseed.Rd | 34 agridat-1.13/agridat/man/silva.cotton.Rd |only agridat-1.13/agridat/man/sinclair.clover.Rd | 12 agridat-1.13/agridat/man/smith.beans.uniformity.Rd |only agridat-1.13/agridat/man/smith.corn.uniformity.Rd | 56 agridat-1.13/agridat/man/snedecor.asparagus.Rd | 182 +- agridat-1.13/agridat/man/snijders.fusarium.Rd | 17 agridat-1.13/agridat/man/stephens.sorghum.uniformity.Rd | 43 agridat-1.13/agridat/man/steptoe.morex.pheno.Rd | 137 + agridat-1.13/agridat/man/stickler.sorghum.uniformity.Rd |only agridat-1.13/agridat/man/stirret.borers.Rd | 4 agridat-1.13/agridat/man/streibig.competition.Rd | 18 agridat-1.13/agridat/man/stroup.nin.Rd | 233 ++ agridat-1.13/agridat/man/stroup.splitplot.Rd | 101 - agridat-1.13/agridat/man/student.barley.Rd | 37 agridat-1.13/agridat/man/tai.potato.Rd |only agridat-1.13/agridat/man/talbot.potato.Rd | 61 agridat-1.13/agridat/man/theobald.barley.Rd | 11 agridat-1.13/agridat/man/theobald.covariate.Rd | 26 agridat-1.13/agridat/man/thompson.cornsoy.Rd | 78 agridat-1.13/agridat/man/turner.herbicide.Rd | 4 agridat-1.13/agridat/man/urquhart.feedlot.Rd |only agridat-1.13/agridat/man/usgs.herbicides.Rd |only agridat-1.13/agridat/man/vaneeuwijk.drymatter.Rd |only agridat-1.13/agridat/man/vaneeuwijk.fusarium.Rd |only agridat-1.13/agridat/man/vaneeuwijk.nematodes.Rd |only agridat-1.13/agridat/man/vargas.txe.Rd | 113 - agridat-1.13/agridat/man/vargas.wheat1.Rd | 166 + agridat-1.13/agridat/man/vargas.wheat2.Rd | 135 - agridat-1.13/agridat/man/verbyla.lupin.Rd | 185 +- agridat-1.13/agridat/man/vold.longterm.Rd | 37 agridat-1.13/agridat/man/vsn.lupin3.Rd | 184 +- agridat-1.13/agridat/man/wallace.iowaland.Rd | 17 agridat-1.13/agridat/man/walsh.cottonprice.Rd | 6 agridat-1.13/agridat/man/wassom.brome.uniformity.Rd |only agridat-1.13/agridat/man/waynick.soil.Rd | 9 agridat-1.13/agridat/man/wedderburn.barley.Rd | 6 agridat-1.13/agridat/man/weiss.incblock.Rd | 31 agridat-1.13/agridat/man/weiss.lattice.Rd | 37 agridat-1.13/agridat/man/welch.bermudagrass.Rd | 3 agridat-1.13/agridat/man/wheatley.carrot.Rd |only agridat-1.13/agridat/man/wiebe.wheat.uniformity.Rd | 37 agridat-1.13/agridat/man/wiedemann.safflower.uniformity.Rd |only agridat-1.13/agridat/man/williams.barley.uniformity.Rd | 36 agridat-1.13/agridat/man/williams.cotton.uniformity.Rd | 39 agridat-1.13/agridat/man/williams.trees.Rd | 4 agridat-1.13/agridat/man/yan.winterwheat.Rd | 29 agridat-1.13/agridat/man/yang.barley.Rd | 38 agridat-1.13/agridat/man/yates.missing.Rd | 24 agridat-1.13/agridat/man/yates.oats.Rd | 148 + agridat-1.13/agridat/man/zuidhof.broiler.Rd | 14 agridat-1.13/agridat/tests |only agridat-1.13/agridat/vignettes/agridat.bib | 44 agridat-1.13/agridat/vignettes/agridat_examples.Rmd |only agridat-1.13/agridat/vignettes/agridat_examples.html |only agridat-1.13/agridat/vignettes/data.Rmd |only agridat-1.13/agridat/vignettes/data.html |only agridat-1.13/agridat/vignettes/papadakis.Rmd |only agridat-1.13/agridat/vignettes/papadakis.html |only 521 files changed, 7306 insertions(+), 4007 deletions(-)
Title: Implementation of an Accountable Data Analysis Process
Description: Tracks reading and writing within R scripts that are organized into
a directed acyclic graph. Contains an interactive shiny application adaprApp().
Uses git2r package, Git and file hashes to track version histories of input
and output. See package vignette for how to get started. V1.02 adds parallel
execution of project scripts and function map in vignette. Makes project
specification argument last in order. V2.0 adds project specific libraries, packrat option, and adaprSheet().
Author: Jon Gelfond, Martin Goros
Maintainer: Jonathan Gelfond <gelfondjal@uthscsa.edu>
Diff between adapr versions 1.0.2 dated 2017-02-02 and 2.0.0 dated 2017-11-29
adapr-1.0.2/adapr/R/id_new_libs.R |only adapr-1.0.2/adapr/R/sync_test_3.R |only adapr-1.0.2/adapr/man/Check.file.hash.Rd |only adapr-1.0.2/adapr/man/Check.file.hash.source.Rd |only adapr-1.0.2/adapr/man/Check.file.mtime.source.Rd |only adapr-1.0.2/adapr/man/Condense.file.info.Rd |only adapr-1.0.2/adapr/man/Create.file.info.Rd |only adapr-1.0.2/adapr/man/Get.file.info.Rd |only adapr-1.0.2/adapr/man/Harvest.trees.Rd |only adapr-1.0.2/adapr/man/ID.sync.Rd |only adapr-1.0.2/adapr/man/Make.dependency.graph.obj.Rd |only adapr-1.0.2/adapr/man/Make.summary.graph.Rd |only adapr-1.0.2/adapr/man/Render_Rmd.Rd |only adapr-1.0.2/adapr/man/Sync.test.OLD.Rd |only adapr-1.0.2/adapr/man/Sync.test.Rd |only adapr-1.0.2/adapr/man/Sync.test.pi.Rd |only adapr-1.0.2/adapr/man/Sync.test_2nd.Rd |only adapr-1.0.2/adapr/man/add_package.Rd |only adapr-1.0.2/adapr/man/commit.project.Rd |only adapr-1.0.2/adapr/man/create_markdown.Rd |only adapr-1.0.2/adapr/man/create_program_graph.Rd |only adapr-1.0.2/adapr/man/create_program_graph_v2.Rd |only adapr-1.0.2/adapr/man/default.adapr.setup.Rd |only adapr-1.0.2/adapr/man/first.project.Rd |only adapr-1.0.2/adapr/man/get.fs.time.Rd |only adapr-1.0.2/adapr/man/get.project.Rd |only adapr-1.0.2/adapr/man/get.project.info.Rd |only adapr-1.0.2/adapr/man/get.project.info.si.Rd |only adapr-1.0.2/adapr/man/get.project.path.Rd |only adapr-1.0.2/adapr/man/get.project.publish.path.Rd |only adapr-1.0.2/adapr/man/get.project.swap.directory.Rd |only adapr-1.0.2/adapr/man/get.pubresults.Rd |only adapr-1.0.2/adapr/man/get_adapr_options.Rd |only adapr-1.0.2/adapr/man/git.add.Rd |only adapr-1.0.2/adapr/man/git.commit.Rd |only adapr-1.0.2/adapr/man/git.configure.Rd |only adapr-1.0.2/adapr/man/git.configure.test.Rd |only adapr-1.0.2/adapr/man/git.history.search.Rd |only adapr-1.0.2/adapr/man/git.info.Rd |only adapr-1.0.2/adapr/man/git.init.Rd |only adapr-1.0.2/adapr/man/git_provenance.Rd |only adapr-1.0.2/adapr/man/graph.project.Rd |only adapr-1.0.2/adapr/man/guess.write.fcn.Rd |only adapr-1.0.2/adapr/man/hashcopy.Rd |only adapr-1.0.2/adapr/man/id_new_libs.Rd |only adapr-1.0.2/adapr/man/init.project.Rd |only adapr-1.0.2/adapr/man/install_project_packages.Rd |only adapr-1.0.2/adapr/man/list.branches.Rd |only adapr-1.0.2/adapr/man/list.datafiles.Rd |only adapr-1.0.2/adapr/man/list.programs.Rd |only adapr-1.0.2/adapr/man/load.install.library.file.Rd |only adapr-1.0.2/adapr/man/load.source.directory.Rd |only adapr-1.0.2/adapr/man/make.hyperlink.Rd |only adapr-1.0.2/adapr/man/make.program.Rd |only adapr-1.0.2/adapr/man/monitorParallelSync.project.Rd |only adapr-1.0.2/adapr/man/open_orchard.Rd |only adapr-1.0.2/adapr/man/parallelSync.project.Rd |only adapr-1.0.2/adapr/man/plant.orchard.Rd |only adapr-1.0.2/adapr/man/plant.tree.Rd |only adapr-1.0.2/adapr/man/program.io.table.Rd |only adapr-1.0.2/adapr/man/project_report_markdown.Rd |only adapr-1.0.2/adapr/man/project_report_send_rmd.Rd |only adapr-1.0.2/adapr/man/pull_source_info.Rd |only adapr-1.0.2/adapr/man/read_library.Rd |only adapr-1.0.2/adapr/man/redirect.tree.Rd |only adapr-1.0.2/adapr/man/relocate.project.Rd |only adapr-1.0.2/adapr/man/remove.program.Rd |only adapr-1.0.2/adapr/man/remove.project.Rd |only adapr-1.0.2/adapr/man/remove_package.Rd |only adapr-1.0.2/adapr/man/report.project.Rd |only adapr-1.0.2/adapr/man/rework.project.path.Rd |only adapr-1.0.2/adapr/man/run.program.Rd |only adapr-1.0.2/adapr/man/send.branch.Rd |only adapr-1.0.2/adapr/man/send.branch.si.Rd |only adapr-1.0.2/adapr/man/send.pubresults.Rd |only adapr-1.0.2/adapr/man/set.project.Rd |only adapr-1.0.2/adapr/man/set_adapr_options.Rd |only adapr-1.0.2/adapr/man/show.project.Rd |only adapr-1.0.2/adapr/man/show.pubresults.Rd |only adapr-1.0.2/adapr/man/show.results.Rd |only adapr-1.0.2/adapr/man/source.sync.si.Rd |only adapr-1.0.2/adapr/man/source_sync_si_load.Rd |only adapr-1.0.2/adapr/man/sprout.program.Rd |only adapr-1.0.2/adapr/man/swap.project.paths.Rd |only adapr-1.0.2/adapr/man/sync.project.Rd |only adapr-1.0.2/adapr/man/sync.test.si.Rd |only adapr-1.0.2/adapr/man/synctest.project.Rd |only adapr-2.0.0/adapr/DESCRIPTION | 22 adapr-2.0.0/adapr/MD5 | 450 ++++++++++--------- adapr-2.0.0/adapr/NAMESPACE | 186 ++++--- adapr-2.0.0/adapr/R/Check_file_hash.R | 12 adapr-2.0.0/adapr/R/Check_file_hash_source.R | 22 adapr-2.0.0/adapr/R/Check_file_mtime_source.R | 19 adapr-2.0.0/adapr/R/Condense_file_info.R | 8 adapr-2.0.0/adapr/R/Digest.R | 4 adapr-2.0.0/adapr/R/Get.file.info.R | 10 adapr-2.0.0/adapr/R/Graph.R | 8 adapr-2.0.0/adapr/R/Harvest_trees.R | 6 adapr-2.0.0/adapr/R/ID_sync.R | 14 adapr-2.0.0/adapr/R/Library.R |only adapr-2.0.0/adapr/R/Make_dependency_graph.R | 10 adapr-2.0.0/adapr/R/Read.R | 24 - adapr-2.0.0/adapr/R/Read_cap.R | 6 adapr-2.0.0/adapr/R/Render.R | 10 adapr-2.0.0/adapr/R/Sync_test_pi.R | 13 adapr-2.0.0/adapr/R/Write.R | 20 adapr-2.0.0/adapr/R/aWrite.R |only adapr-2.0.0/adapr/R/adaprInstall.R |only adapr-2.0.0/adapr/R/adaprSheet.R |only adapr-2.0.0/adapr/R/adapr_update.R |only adapr-2.0.0/adapr/R/add_library.R | 54 -- adapr-2.0.0/adapr/R/commit_project.R | 34 - adapr-2.0.0/adapr/R/create_file_info.R | 8 adapr-2.0.0/adapr/R/create_markdown.R | 39 - adapr-2.0.0/adapr/R/create_program_graph.R | 16 adapr-2.0.0/adapr/R/create_program_graph_2.R | 85 --- adapr-2.0.0/adapr/R/create_source_file_dir.R | 51 +- adapr-2.0.0/adapr/R/default_setup.R | 190 +++++--- adapr-2.0.0/adapr/R/dependency_class.R | 1 adapr-2.0.0/adapr/R/file_delay.R | 8 adapr-2.0.0/adapr/R/finalize_dependency.R | 29 - adapr-2.0.0/adapr/R/get.adapr.options.R | 134 +---- adapr-2.0.0/adapr/R/get.fs.time.R | 13 adapr-2.0.0/adapr/R/get.orchard.R | 94 +++ adapr-2.0.0/adapr/R/get_project_info.R | 12 adapr-2.0.0/adapr/R/get_project_info_si.R | 12 adapr-2.0.0/adapr/R/get_project_path.R | 75 ++- adapr-2.0.0/adapr/R/get_project_swap_directory.R | 6 adapr-2.0.0/adapr/R/git.commit.R | 11 adapr-2.0.0/adapr/R/gitIngoreLibrary.R |only adapr-2.0.0/adapr/R/git_add.R | 9 adapr-2.0.0/adapr/R/git_config_test.R | 30 - adapr-2.0.0/adapr/R/git_configure.R | 10 adapr-2.0.0/adapr/R/git_history_search.R | 9 adapr-2.0.0/adapr/R/git_info.R | 7 adapr-2.0.0/adapr/R/git_init.R | 7 adapr-2.0.0/adapr/R/git_path.R | 2 adapr-2.0.0/adapr/R/git_provenance.R | 17 adapr-2.0.0/adapr/R/guess_write_fnc.R | 14 adapr-2.0.0/adapr/R/guress_read_fcn.R | 1 adapr-2.0.0/adapr/R/hashcopy.R | 68 +- adapr-2.0.0/adapr/R/hashtags.R | 13 adapr-2.0.0/adapr/R/id_new_packages.R |only adapr-2.0.0/adapr/R/importData.R |only adapr-2.0.0/adapr/R/intialize.dependency.info.R | 49 -- adapr-2.0.0/adapr/R/list_files.R | 251 +++------- adapr-2.0.0/adapr/R/load_branch.R | 79 +++ adapr-2.0.0/adapr/R/load_install_library_file.R | 185 +++++++ adapr-2.0.0/adapr/R/load_source_directory.R | 8 adapr-2.0.0/adapr/R/makeFunction.R |only adapr-2.0.0/adapr/R/make_hyperlink.R | 8 adapr-2.0.0/adapr/R/make_source_info.R | 6 adapr-2.0.0/adapr/R/make_summary_graph.R | 14 adapr-2.0.0/adapr/R/openScript.R |only adapr-2.0.0/adapr/R/parallelsync_project.R | 65 -- adapr-2.0.0/adapr/R/path_expand.2.R | 26 - adapr-2.0.0/adapr/R/plant_orchard.R | 21 adapr-2.0.0/adapr/R/plant_tree.R | 99 ++-- adapr-2.0.0/adapr/R/powerSyncProject.R |only adapr-2.0.0/adapr/R/program_io_table.R | 7 adapr-2.0.0/adapr/R/project_report_markdown.R | 69 -- adapr-2.0.0/adapr/R/project_report_send_rmd.R | 84 --- adapr-2.0.0/adapr/R/publishers.R | 29 - adapr-2.0.0/adapr/R/rapidPlot.R |only adapr-2.0.0/adapr/R/read_dependency.R | 6 adapr-2.0.0/adapr/R/rework_project_path.R | 9 adapr-2.0.0/adapr/R/run_Program.R | 59 +- adapr-2.0.0/adapr/R/scriptSubgraph.R |only adapr-2.0.0/adapr/R/script_loader.R | 7 adapr-2.0.0/adapr/R/searchScripts.R |only adapr-2.0.0/adapr/R/send_branch.R | 8 adapr-2.0.0/adapr/R/send_branch_si.R | 7 adapr-2.0.0/adapr/R/setProject.R |only adapr-2.0.0/adapr/R/shinyTree.R | 3 adapr-2.0.0/adapr/R/source_sync_si.R | 39 - 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adapr-2.0.0/adapr/man/syncTrunk.Rd |only adapr-2.0.0/adapr/man/updateAdaprConfig.Rd |only adapr-2.0.0/adapr/man/write.dependency.Rd | 5 adapr-2.0.0/adapr/vignettes/ADAPRVignette.Rmd | 157 ++---- 333 files changed, 2470 insertions(+), 2780 deletions(-)
Title: Command Line Optional and Positional Argument Parser
Description: A command line parser to
be used with Rscript to write "#!" shebang scripts that gracefully
accept positional and optional arguments and automatically generate usage.
Author: Trevor L Davis. Ports examples from the argparse Python module by the
Python Software Foundation. Ports examples from the getopt package by Allen
Day.
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between argparse versions 1.0.7 dated 2017-08-22 and 1.1.0 dated 2017-11-29
DESCRIPTION | 11 +-- INSTALL | 11 +++ MD5 | 22 ++++--- NAMESPACE | 2 NEWS | 12 ++++ R/argparse.R | 117 ++++++++++++++++++++++++----------------- inst/COPYRIGHTS | 2 inst/doc/argparse.html | 56 ++++++++++--------- man/ArgumentParser.Rd | 12 ++-- tests/test_help.R |only tests/test_help.Rout.save |only tests/test_version.R |only tests/test_version.Rout.save |only tests/testthat/test-argparse.R | 85 ++++++++++++++++++++++------- 14 files changed, 211 insertions(+), 119 deletions(-)
Title: Monetary Unit Sampling and Estimation Methods, Widely Used in
Auditing
Description: Sampling and evaluation methods to apply Monetary Unit Sampling (or in older literature Dollar Unit Sampling) during an audit of financial statements.
Author: Henning Prömpers, André Guimarães
Maintainer: Henning Prömpers <henning@proempers.net>
Diff between MUS versions 0.1.4 dated 2017-05-29 and 0.1.5 dated 2017-11-29
DESCRIPTION | 13 + MD5 | 47 ++++- NAMESPACE | 4 R/MUS.bounds.R |only R/MUS.combine.R |only R/MUS.evaluation.R | 151 +++++++++++++++---- R/MUS.extend.R |only R/MUS.extraction.R | 22 +- R/MUS.planning.R | 64 +++++++- R/print.MUS.evaluation.result.R | 283 +++++++++++++++++++++++++++++++----- R/print.MUS.extraction.result.R |only R/print.MUS.planning.result.R |only build/partial.rdb |binary inst |only man/MUS.binomial.bound.Rd |only man/MUS.calc.n.conservative.Rd |only man/MUS.combine.Rd |only man/MUS.combined.high.error.rate.Rd |only man/MUS.evaluation.Rd | 9 + man/MUS.extend.Rd |only man/MUS.extraction.Rd | 7 man/MUS.factor.Rd |only man/MUS.moment.bound.Rd |only man/MUS.multinomial.bound.Rd |only man/MUS.planning.Rd | 12 + man/examples |only man/print.MUS.evaluation.result.Rd | 12 + man/print.MUS.extraction.result.Rd |only man/print.MUS.planning.result.Rd |only po |only 30 files changed, 514 insertions(+), 110 deletions(-)
Title: Diverse Cluster Ensemble in R
Description: Performs cluster analysis using an ensemble clustering framework.
Results from a diverse set of algorithms are pooled together using methods
such as majority voting, K-Modes, LinkCluE, and CSPA. There are options to
compare cluster assignments across algorithms using internal and external
indices, visualizations such as heatmaps, and significance testing for the
existence of clusters.
Author: Derek Chiu [aut, cre],
Aline Talhouk [aut],
Johnson Liu [ctb, com]
Maintainer: Derek Chiu <dchiu@bccrc.ca>
Diff between diceR versions 0.2.0 dated 2017-09-29 and 0.3.0 dated 2017-11-29
DESCRIPTION | 22 - MD5 | 32 - NEWS.md | 14 R/consensus_combine.R | 2 R/consensus_evaluate.R | 338 ++++++++------- R/dice.R | 27 - R/graphs.R | 74 ++- inst/doc/overview.R | 30 - inst/doc/overview.Rmd | 110 ++++- inst/doc/overview.html | 702 ++++++++++++++++---------------- man/consensus_combine.Rd | 2 man/consensus_evaluate.Rd | 13 man/dice.Rd | 4 man/graphs.Rd | 4 tests/testthat/test-consensus_combine.R | 2 tests/testthat/test-dice.R | 13 vignettes/overview.Rmd | 110 ++++- 17 files changed, 910 insertions(+), 589 deletions(-)
Title: Take Screenshots of Web Pages
Description: Takes screenshots of web pages, including Shiny applications and R
Markdown documents.
Author: Winston Chang [aut, cre],
Yihui Xie [ctb],
Francois Guillem [ctb],
Nicolas Perriault [ctb] (The CasperJS library)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between webshot versions 0.4.2 dated 2017-09-25 and 0.5.0 dated 2017-11-29
DESCRIPTION | 13 +++++++------ MD5 | 18 ++++++++++-------- NAMESPACE | 1 + NEWS.md | 7 +++++++ R/appshot.R | 42 ++++++------------------------------------ R/rmdshot.R |only R/utils.R | 28 +++++++++++++++++++--------- README.md | 22 +++++++++++++++++----- build/vignette.rds |binary inst/doc/intro.html | 22 ++++++++++++---------- man/rmdshot.Rd |only 11 files changed, 79 insertions(+), 74 deletions(-)
Title: Unicode Text Processing
Description: Processing and printing 'UTF-8' encoded international text (Unicode). Functions to input, validate, normalize, encode, format, and display.
Author: Patrick O. Perry [aut, cph, cre],
Unicode, Inc. [cph, dtc] (Unicode Character Database)
Maintainer: Patrick O. Perry <pperry@stern.nyu.edu>
Diff between utf8 versions 1.1.0 dated 2017-11-20 and 1.1.1 dated 2017-11-29
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 12 ++++++++++-- README.md | 6 +++--- src/as_utf8.c | 6 ++++-- 5 files changed, 24 insertions(+), 14 deletions(-)
Title: Particle Tracking and Demography
Description: Obtain population density and body size structure, using video material or image sequences as input. Functions assist in the creation of image sequences from videos, background detection and subtraction, particle identification and tracking. An artificial neural network can be trained for noise filtering. The goal is to supply accurate estimates of population size, structure and/or individual behavior, for use in evolutionary and ecological studies.
Author: Marjolein Bruijning, Marco D. Visser, Caspar A. Hallmann, Eelke Jongejans
Maintainer: Marjolein Bruijning <m.bruijning@science.ru.nl>
Diff between trackdem versions 0.2 dated 2017-06-27 and 0.3 dated 2017-11-29
trackdem-0.2/trackdem/src/init.c |only trackdem-0.3/trackdem/DESCRIPTION | 10 trackdem-0.3/trackdem/MD5 | 146 +++- trackdem-0.3/trackdem/NAMESPACE | 2 trackdem-0.3/trackdem/R/RcppExports.R | 14 trackdem-0.3/trackdem/R/help.R | 4 trackdem-0.3/trackdem/R/identifyFunctions.R | 548 ++++++++++++---- trackdem-0.3/trackdem/R/nnFunctions.R | 787 ++++++++++++++---------- trackdem-0.3/trackdem/R/resultsFunctions.R | 233 ++++--- trackdem-0.3/trackdem/R/simulationFunctions.R | 494 +++++++-------- trackdem-0.3/trackdem/R/trackFunctions.R | 230 ++++++- trackdem-0.3/trackdem/inst |only trackdem-0.3/trackdem/man/createBackground.Rd | 21 trackdem-0.3/trackdem/man/createImageSeq.Rd | 17 trackdem-0.3/trackdem/man/findThreshold.Rd |only trackdem-0.3/trackdem/man/identifyParticles.Rd | 57 + trackdem-0.3/trackdem/man/loadImages.Rd | 20 trackdem-0.3/trackdem/man/manuallySelect.Rd | 42 - trackdem-0.3/trackdem/man/mergeTracks.Rd |only trackdem-0.3/trackdem/man/plot.TrDm.Rd | 18 trackdem-0.3/trackdem/man/runBatch.Rd | 37 - trackdem-0.3/trackdem/man/simulTrajec.Rd | 31 trackdem-0.3/trackdem/man/subtractBackground.Rd | 18 trackdem-0.3/trackdem/man/summary.TrDm.Rd | 9 trackdem-0.3/trackdem/man/testNN.Rd | 27 trackdem-0.3/trackdem/man/trackParticles.Rd | 31 trackdem-0.3/trackdem/man/trackdem.Rd | 6 trackdem-0.3/trackdem/man/update.particles.Rd | 37 + trackdem-0.3/trackdem/src/RcppExports.cpp | 39 + trackdem-0.3/trackdem/src/sb.cpp | 1 trackdem-0.3/trackdem/src/sb2.cpp |only 31 files changed, 1929 insertions(+), 950 deletions(-)
More information about LSDsensitivity at CRAN
Permanent link
Title: Efficient Phylogenetics on Large Trees
Description: Efficient tree manipulations for large phylogenies, including pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism). Ancestral state reconstruction and hidden character prediction of discrete characters, using Maximum Likelihood and Maximum Parsimony methods. Simulating and fitting models of trait evolution, and generating random trees using birth-death models.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@zoology.ubc.ca>
Diff between castor versions 1.2.2 dated 2017-09-27 and 1.3 dated 2017-11-29
DESCRIPTION | 10 MD5 | 108 +- NAMESPACE | 12 R/RcppExports.R | 32 R/asr_empirical_probabilities.R | 2 R/asr_independent_contrasts.R | 23 R/asr_max_parsimony.R | 2 R/asr_mk_model.R | 25 R/asr_squared_change_parsimony.R | 7 R/auxiliary_routines.R | 72 - R/collapse_monofurcations.R |only R/count_clades_over_time.R | 9 R/extend_tree_to_height.R |only R/find_farthest_tips.R |only R/find_nearest_tips.R | 8 R/find_root_of_monophyletic_tips.R |only R/fit_tree_model.R | 151 ++- R/generate_random_tree.R | 9 R/get_all_node_depths.R |only R/get_independent_contrasts.R | 11 R/get_subtree_at_node.R | 3 R/hsp_empirical_probabilities.R | 3 R/hsp_independent_contrasts.R | 6 R/hsp_max_parsimony.R | 3 R/hsp_mk_model.R | 12 R/hsp_squared_change_parsimony.R | 4 R/reconstruct_past_diversification.R | 66 + R/root_at_midpoint.R |only R/root_in_edge.R |only R/root_via_outgroup.R | 13 R/simulate_diversification_model.R | 46 - inst/CITATION | 3 man/asr_independent_contrasts.Rd | 26 man/asr_mk_model.Rd | 3 man/castor.Rd | 2 man/collapse_monofurcations.Rd |only man/count_clades_over_time.Rd | 15 man/extend_tree_to_height.Rd |only man/find_farthest_tips.Rd |only man/find_nearest_tips.Rd | 18 man/find_root.Rd | 11 man/find_root_of_monophyletic_tips.Rd |only man/fit_tree_model.Rd |only man/generate_random_tree.Rd | 6 man/generate_tree_with_evolving_rates.Rd | 2 man/get_all_node_depths.Rd |only man/get_independent_contrasts.Rd | 24 man/get_trait_acf.Rd | 4 man/hsp_empirical_probabilities.Rd | 4 man/hsp_independent_contrasts.Rd | 4 man/hsp_max_parsimony.Rd | 4 man/hsp_mk_model.Rd | 9 man/hsp_squared_change_parsimony.Rd | 4 man/multifurcations_to_bifurcations.Rd | 5 man/reconstruct_past_diversification.Rd |only man/root_at_midpoint.Rd |only man/root_at_node.Rd | 3 man/root_in_edge.Rd |only man/root_via_outgroup.Rd | 11 man/simulate_diversification_model.Rd | 39 man/trim_tree_at_height.Rd | 3 src/RcppExports.cpp | 126 ++ src/phylogenetics_cpp_routines.cpp | 1411 ++++++++++++++++++++++++++----- 63 files changed, 1862 insertions(+), 512 deletions(-)
Title: Bayesian Multilevel Mediation
Description: Easy estimation of Bayesian multilevel mediation models with Stan.
Author: Matti Vuorre [aut, cre] (0000-0001-5052-066X)
Maintainer: Matti Vuorre <mv2521@columbia.edu>
Diff between bmlm versions 1.3.4 dated 2017-11-21 and 1.3.5 dated 2017-11-29
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ src/Modules.cpp | 4 ++-- tools/make_cpp.R | 2 +- 5 files changed, 15 insertions(+), 11 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-01-28 1.0
Title: Multivariate Ordinal Regression Models
Description: A flexible framework for fitting multivariate
ordinal regression models with composite likelihood methods.
Author: Rainer Hirk [aut, cre],
Kurt Hornik [aut],
Laura Vana [aut],
Alan Genz [ctb] (Fortran Code)
Maintainer: Rainer Hirk <rhirk@wu.ac.at>
Diff between mvord versions 0.2.0 dated 2017-11-10 and 0.2.1 dated 2017-11-29
DESCRIPTION | 8 - MD5 | 41 ++++----- NAMESPACE | 1 NEWS | 6 + R/error_struct.R | 85 ++++++++++++++++-- R/mvlinks.R | 20 ++-- R/mvord.R | 157 +++++++++++++++++----------------- R/mvord_fit.R | 89 +++++++++++-------- R/predict.R | 192 ++++++++++++++++++++++++++++++++---------- R/se.R | 194 ++++++++++++++++++++++++++++--------------- R/utilities.R | 104 ++++++++++++++++------- inst/doc/vignette_mvord.R | 64 +++++++------- inst/doc/vignette_mvord.Rnw | 63 +++++++++++-- inst/doc/vignette_mvord.pdf |binary man/error_struct.Rd | 3 man/mvord.Rd | 6 - man/mvord2.Rd | 6 - man/names_constraints.Rd | 4 tests/check_methods.R |only tests/check_mvord_data.R | 20 ++-- tests/check_toy_example.R | 79 +++++++++++++---- vignettes/vignette_mvord.Rnw | 63 +++++++++++-- 22 files changed, 819 insertions(+), 386 deletions(-)
Title: Heteroskedastic Gaussian Process Modeling and Design under
Replication
Description: Performs Gaussian process regression with heteroskedastic noise following Binois, M., Gramacy, R., Ludkovski, M. (2016) <arXiv:1611.05902>. The input dependent noise is modeled as another Gaussian process. Replicated observations are encouraged as they yield computational savings. Sequential design procedures based on the integrated mean square prediction error and lookahead heuristics are provided, and notably fast update functions when adding new observations.
Author: Mickael Binois, Robert B. Gramacy
Maintainer: Mickael Binois <mickael.binois@chicagobooth.edu>
Diff between hetGP versions 1.0.0 dated 2017-09-28 and 1.0.1 dated 2017-11-29
DESCRIPTION | 8 +- MD5 | 52 ++++++++------ NAMESPACE | 10 ++ NEWS |only R/IMSE.R | 27 ++++--- R/TestFunctions.R | 6 - R/hetGP-package.R | 153 +++++++++++++++++++++++++------------------- R/hetGP.R | 163 ++++++++++++++++++++++++----------------------- R/hetTP.R |only R/update_hetGP.R | 5 + man/IMSE.search.Rd | 6 - man/IMSE_nsteps_ahead.Rd | 4 - man/SIR.Rd | 6 - man/allocate_mult.Rd | 5 - man/compareGP.Rd | 4 - man/crit_IMSE.Rd | 6 - man/deriv_crit_IMSE.Rd | 2 man/find_reps.Rd | 4 - man/hetGP-package.Rd | 149 +++++++++++++++++++++++++----------------- man/mleHetGP.Rd | 36 +++++----- man/mleHetTP.Rd |only man/mleHomGP.Rd | 9 +- man/mleHomTP.Rd |only man/predict.hetTP.Rd |only man/predict.homGP.Rd | 4 - man/predict.homTP.Rd |only man/update_horizon.Rd | 4 - src/EMSE.cpp | 114 ++++++++++++++++---------------- src/Matern_utils.cpp | 24 +++--- src/distcpp.cpp | 23 ------ 30 files changed, 441 insertions(+), 383 deletions(-)
Title: Sensitivity Analyses for Unmeasured Confounding in Observational
Studies and Meta-Analyses
Description: Conducts sensitivity analyses for unmeasured confounding for either an observational study or a meta-analysis of observational studies. For a single observational study, the package reports E-values, defined as the minimum strength of association on the risk ratio scale that an unmeasured confounder would need to have with both the treatment and the outcome to fully explain away a specific treatment-outcome association, conditional on the measured covariates. One can use one of the evalues.XX() functions to compute E-values for the relevant outcome types. Outcome types include risk ratios, odds ratio with common or rare outcomes, hazard ratios with common or rare outcomes, and standardized differences in outcomes. Optionally, one can use the bias_plot() function to plot the bias factor as a function of two sensitivity parameters. (See VanderWeele & Ding, 2017 [<http://annals.org/aim/article/2643434>] for details.) For a meta-analysis, use the function confounded_meta to compute point estimates and inference for: (1) the proportion of studies with true causal effect sizes more extreme than a specified threshold of scientific importance; and (2) the minimum bias factor and confounding strength required to reduce to less than a specified threshold the proportion of studies with true effect sizes of scientifically significant size. The functions sens_plot() and sens_table() create plots and tables for visualizing these meta-analysis metrics across a range of bias values, and scrape_meta helps scrape study-level data from a published forest plot or summary table to obtain the needed estimates when these are not reported. (See Mathur & VanderWeele [<https://osf.io/jkhfg/>] for details.) Most of the analyses available in this package can also be conducted using web-based graphical interfaces (for a single observational study: <https://mmathur.shinyapps.io/evalue/>; for a meta-analysis: <https://mmathur.shinyapps.io/meta_gui_2/>).
Author: Maya B. Mathur, Peng Ding, Tyler J. VanderWeele
Maintainer: Maya B. Mathur <mmathur@stanford.edu>
Diff between EValue versions 1.0.0 dated 2017-10-30 and 1.1.0 dated 2017-11-29
EValue-1.0.0/EValue/man/biasPlot.Rd |only EValue-1.1.0/EValue/DESCRIPTION | 11 EValue-1.1.0/EValue/MD5 | 29 - EValue-1.1.0/EValue/NAMESPACE | 2 EValue-1.1.0/EValue/R/EValue.R | 567 +++++++++++++++-------------- EValue-1.1.0/EValue/man/bias_plot.Rd |only EValue-1.1.0/EValue/man/confounded_meta.Rd | 56 +- EValue-1.1.0/EValue/man/evalues.HR.Rd | 2 EValue-1.1.0/EValue/man/evalues.MD.Rd | 2 EValue-1.1.0/EValue/man/evalues.OR.Rd | 2 EValue-1.1.0/EValue/man/evalues.RD.Rd | 2 EValue-1.1.0/EValue/man/scrape_meta.Rd | 10 EValue-1.1.0/EValue/man/sens_plot.Rd | 64 +-- EValue-1.1.0/EValue/man/sens_table.Rd | 62 +-- EValue-1.1.0/EValue/man/stronger_than.Rd | 27 - EValue-1.1.0/EValue/man/threshold.Rd | 3 EValue-1.1.0/EValue/tests |only 17 files changed, 432 insertions(+), 407 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-12 2.0.23
2015-06-19 2.0.22
2015-06-18 2.0.20
2015-06-17 2.0.17