Title: Base Package for Phylogenetic Structures and Comparative Data
Description: Provides a base S4 class for comparative methods, incorporating
one or more trees and trait data.
Author: R Hackathon et al. (alphabetically: Ben Bolker, Marguerite Butler,
Peter Cowan, Damien de Vienne, Dirk Eddelbuettel, Mark Holder, Thibaut
Jombart, Steve Kembel, Francois Michonneau, David Orme, Brian O'Meara,
Emmanuel Paradis, Jim Regetz, Derrick Zwickl)
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between phylobase versions 0.8.2 dated 2016-01-22 and 0.8.4 dated 2017-04-21
DESCRIPTION | 8 +- MD5 | 109 +++++++++++++++--------------- NAMESPACE | 4 - NEWS.md | 3 R/RcppExports.R | 2 R/ancestors.R | 4 - R/phylobase-package.R | 2 R/print-methods.R | 1 R/subset-methods.R | 30 ++++---- build/vignette.rds |binary inst/doc/phylobase.pdf |binary man/MRCA.Rd | 3 man/addData-methods.Rd | 19 ++--- man/ancestors.Rd | 4 - man/checkPhylo4.Rd | 9 +- man/edgeLength-methods.Rd | 22 +++--- man/edges-accessors.Rd | 17 ++-- man/extractTree.Rd | 7 - man/formatData.Rd | 7 - man/geospiza.Rd | 1 man/getNode-methods.Rd | 8 +- man/labels-methods.Rd | 30 ++++---- man/multiPhylo-class.Rd | 5 + man/nTips-methods.Rd | 11 +-- man/nodeId-methods.Rd | 5 - man/owls4.Rd | 1 man/pdata-class.Rd | 14 +-- man/pdata.Rd | 9 +- man/phylo4-class.Rd | 8 +- man/phylo4-methods.Rd | 19 ++--- man/phylo4d-accessors.Rd | 14 +-- man/phylo4d-class.Rd | 8 +- man/phylo4d-methods.Rd | 36 +++++----- man/phyloXXYY.Rd | 7 - man/phylobase-package.Rd | 4 - man/phylobase.options.Rd | 1 man/phylobubbles.Rd | 11 +-- man/phylomat-class.Rd | 7 + man/plotOneTree.Rd | 7 - man/print-methods.Rd | 13 +-- man/readNexus.Rd | 9 +- man/reorder-methods.Rd | 13 +-- man/root-methods.Rd | 2 man/setAs-methods.Rd | 24 ++++-- man/shortestPath-methods.Rd | 5 - man/subset-methods.Rd | 22 ++---- man/summary-methods.Rd | 17 ++-- man/tdata-methods.Rd | 41 ++++++----- man/tip.data.plot.Rd | 1 man/treePlot-methods.Rd | 23 +++--- man/treeStructure-methods.Rd | 9 +- src/RcppExports.cpp | 154 +++++++++++++++++++++---------------------- src/ancestors.c | 4 - src/descendants.c | 6 - src/phylobase_init.c |only vignettes/auto/phylobase.el | 7 + 56 files changed, 405 insertions(+), 402 deletions(-)
Title: Formalized Plots for Self-Describing Data
Description: Creates fully-annotated plots with minimum guidance.
Since the data is self-describing, less effort is needed for
creating the plot. Generally expects data of class folded
(see fold package). If attributes GUIDE and LABEL are present,
they will be used to create formal axis labels. Several aesthetics
are supported, such as reference lines, unity lines, smooths, and
log transformations.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between metaplot versions 0.1.1 dated 2017-04-17 and 0.1.2 dated 2017-04-21
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/metaplot.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Spatial and Network Based Individual Level Models for Epidemics
Description: Provides tools for simulating from discrete-time individual level models for infectious disease data analysis. This epidemic model class contains spatial and contact-network based models with two disease types: Susceptible-Infectious (SI) and Susceptible-Infectious-Removed (SIR).
Author: Vineetha Warriyar. K. V. and Rob Deardon
Maintainer: Vineetha Warriyar. K. V. <vineethawarriyar.kod@ucalgary.ca>
Diff between EpiILM versions 1.1 dated 2017-04-17 and 1.2 dated 2017-04-21
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/epidata.r | 4 ++-- R/epilike.r | 4 ++-- man/epidata.Rd | 5 ++--- src/Epidata.f95 | 4 ++-- 6 files changed, 18 insertions(+), 19 deletions(-)
Title: Data Table Back-End for 'dplyr'
Description: This implements the data table back-end for 'dplyr' so that you
can seamlessly use data table and 'dplyr' together.
Author: Lionel Henry [cre],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between dtplyr versions 0.0.1 dated 2016-06-27 and 0.0.2 dated 2017-04-21
DESCRIPTION | 16 +++++---- MD5 | 30 +++++++++--------- NAMESPACE | 58 +++--------------------------------- NEWS.md | 6 +++ R/compat-dplyr-0.6.0.R |only R/do.R | 12 +++++-- R/grouped-dt.r | 14 +------- R/joins.R | 12 ------- R/sample.R | 6 --- R/sets.R | 7 ++-- R/tbl-dt.r | 69 ++++++++++++++++++++----------------------- README.md | 9 ++++- man/grouped_dt.Rd | 1 man/join.tbl_dt.Rd | 7 +--- man/src_local.Rd | 1 man/tbl_dt.Rd | 3 - tests/testthat/helper-data.R |only 17 files changed, 97 insertions(+), 154 deletions(-)
Title: Retrieval, Analysis, and Anomaly Calculation of Daily Hydrologic
Time Series Data
Description: Imports U.S. Geological Survey (USGS) daily hydrologic data from USGS web services (see <https://waterservices.usgs.gov/> for more information), plots the data, addresses some common data problems, and calculates and plots anomalies.
Author: Karen R. Ryberg and Aldo V. Vecchia
Maintainer: Karen R. Ryberg <kryberg@usgs.gov>
Diff between waterData versions 1.0.6 dated 2017-02-13 and 1.0.7 dated 2017-04-21
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ NEWS | 4 ++++ R/importDVs.R | 10 ++++++---- R/waterData-package.R | 4 ++-- build/vignette.rds |binary data/exampleWaterData.RData |binary inst/doc/vignette.R | 2 +- inst/doc/vignette.Rnw | 2 +- inst/doc/vignette.pdf |binary man/plotParam.Rd | 2 +- man/waterData-package.Rd | 4 ++-- vignettes/vignette.Rnw | 2 +- 13 files changed, 35 insertions(+), 29 deletions(-)
Title: Student Growth Percentiles & Percentile Growth Trajectories
Description: Functions to calculate student growth percentiles and percentile growth projections/trajectories for students using large scale,
longitudinal assessment data. Functions use quantile regression to estimate the conditional density associated
with each student's achievement history. Percentile growth projections/trajectories are calculated using the coefficient matrices derived from
the quantile regression analyses and specify what percentile growth is required for students to reach future achievement targets.
Author: Damian W. Betebenner [aut, cre],
Adam R. Van Iwaarden [aut],
Ben Domingue [aut],
Yi Shang [aut],
Jonathan Weeks [ctb],
John Stewart [ctb],
Jinnie Choi [ctb],
Xin Wei [ctb],
Hi Shin Shim [ctb],
Xiaoyuan Tan [ctb] (Arizona Department of Education),
Carrie Giovannini [ctb] (Arizona Department of Education),
Sarah Polasky [ctb] (Arizona State University),
Rebecca Gau [ctb] (Arizona Charter School Association),
Jeffrey Dean [ctb] (University of Arkansas),
William Bonk [ctb] (Colorado Department of Education),
Marie Huchton [ctb] (Colorado Department of Education),
Allison Timberlake [ctb] (Georgia Department of Education),
Qi Qin [ctb] (Georgia Department of Education),
Melissa Fincher [ctb] (Georgia Department of Education),
Kiran Athota [ctb] (Georgia Department of Education),
Travis Allen [ctb] (Georgia Department of Education),
Glenn Hirata [ctb] (Hawaii Department of Education),
Glenn Nochi [ctb] (Hawaii Department of Education),
Joshua Lee [ctb] (Hawaii Department of Education),
Ayaka Nukui [ctb] (Idaho Department of Education),
Carissa Miller [ctb] (Idaho Department of Education),
Matthew Raimondi [ctb] (Elgin Area School District U46 (Illinois)),
Wes Bruce [ctb] (Indiana Department of Education),
Robert Hochsegang [ctb] (Indiana Department of Education),
Tony Moss [ctb] (Kansas State Department of Education),
Xuewen Sheng [ctb] (Kansas State Department of Education),
Kathy Flanagan [ctb] (Massachusetts Department of Elementary and Secondary Education),
Robert Lee [ctb] (Massachusetts Department of Elementary and Secondary Education),
Ji Zeng [ctb] (Michigan Department of Education),
Steve Viger [ctb] (Michigan Department of Education),
Joe DeCastra [ctb] (Mississippi Department of Education),
Ken Thompson [ctb] (Mississippi Department of Education),
Soo Yeon Cho [ctb] (Missouri Department of Education),
Jeff Halsell [ctb] (Clark County School District, Nevada),
Selcuk Ozdemir [ctb] (Washoe County School District, Nevada),
Roger Silva [ctb] (Nevada Department of Education),
Deb Wiswell [ctb] (New Hampshire Department of Education),
Katya Levitan-Reiner [ctb] (New Haven Public Schools),
Catherine McCaslin [ctb] (New Haven Public Schools),
Joshua Marland [ctb] (New York Education Department),
W Joshua Rew [ctb] (Oregon Department of Education),
Jason Becker [ctb] (Rhode Island Department of Education),
Jessica Bailey [ctb] (Rhode Island Department of Education),
Ana Karantonis [ctb] (Rhode Island Department of Education),
Deborah Jonas [ctb] (Virginia Department of Education),
Juan D'Brot [ctb] (West Virginia Department of Education),
Nate Hixson [ctb] (West Virginia Department of Education),
Deb Came [ctb] (Washington Office of Superintendent of Public Instruction),
Ashley Colburn [ctb] (Washington Office of Superintendent of Public Instruction),
Nick Hassell [ctb] (Washington Office of Superintendent of Public Instruction),
Krissy Johnson [ctb] (Washington Office of Superintendent of Public Instruction),
Daniel Bush [ctb] (Wisconsin Department of Education),
Justin Meyer [ctb] (Wisconsin Department of Education),
Joseph Newton [ctb] (Wisconsin Department of Education),
Nick Stroud [ctb] (Wisconsin Department of Education),
John Paul [ctb] (Wyoming Department of Education),
Michael Flicek [ctb] (Michael Flicek Projects LLC working with Wyoming Department of Education),
Phyllis Clay [ctb] (Albuquerque Public Schools),
Peter Kinyua [ctb] (Albuquerque Public Schools),
Brendan Houng [ctb] (University of Melbourne, Australia, NAPLAN),
Leslie Rosale [ctb] (Ministry of Education, Guatemala),
Nathan Wall [ctb] (eMetric working with Nevada Department of Education and South Dakota Department of Education),
Narek Sahakyan [ctb] (World Class Instruction and Design (WIDA))
Maintainer: Damian W. Betebenner <dbetebenner@nciea.org>
Diff between SGP versions 1.6-0.0 dated 2017-01-01 and 1.7-0.0 dated 2017-04-21
DESCRIPTION | 14 MD5 | 85 +- R/abcSGP.R | 30 - R/analyzeSGP.R | 404 ++++++------- R/checkSGP.R | 81 ++ R/combineSGP.R | 159 ++++- R/courseProgressionSGP.R | 5 R/createUniqueLongData.R | 98 ++- R/getAchievementLevel.R | 22 R/getKey.R | 6 R/getKnotsBoundaries.R | 22 R/getPanelData.R | 260 +++++++- R/getPanelDataVnames.R | 82 +- R/getPreferredSGP.R | 9 R/getSGPConfig.R | 2 R/getStateAbbreviation.R | 28 R/getTargetSGP.R | 96 ++- R/getTargetScaleScore.R | 99 ++- R/gofSGP.R | 28 R/growthAchievementPlot.R | 10 R/outputSGP.R | 45 - R/prepareSGP.R | 26 R/rliCutscoreCreation.R |only R/rliSGP.R | 54 + R/sqliteSGP.R | 12 R/studentGrowthPercentiles.R | 84 ++ R/studentGrowthProjections.R | 46 + R/summarizeSGP.R | 51 + R/summarizeSGP_Utilities.R | 4 R/testSGP.R | 1195 +++++++++++++++++++++++++++++++++------- R/updateSGP.R | 20 R/visualizeSGP.R | 10 R/zzz.R | 4 data/SGPstateData.rda |binary inst/CITATION | 10 inst/NEWS | 6 man/SGP-package.Rd | 23 man/abcSGP.Rd | 27 man/analyzeSGP.Rd | 13 man/combineSGP.Rd | 18 man/rliSGP.Rd | 11 man/studentGrowthPercentiles.Rd | 19 man/studentGrowthProjections.Rd | 13 man/updateSGP.Rd | 24 44 files changed, 2433 insertions(+), 822 deletions(-)
Title: Fit Continuous-Time Correlated Random Walk Models to Animal
Movement Data
Description: Fit continuous-time
correlated random walk models with time indexed
covariates to animal telemetry data. The model is fit using the Kalman-filter on
a state space version of the continuous-time stochastic
movement process.
Author: Devin S. Johnson
Maintainer: Devin S. Johnson <devin.johnson@noaa.gov>
Diff between crawl versions 2.0.1 dated 2016-07-29 and 2.1.1 dated 2017-04-21
crawl-2.0.1/crawl/build |only crawl-2.0.1/crawl/demo |only crawl-2.0.1/crawl/inst |only crawl-2.0.1/crawl/vignettes |only crawl-2.1.1/crawl/DESCRIPTION | 23 ++--- crawl-2.1.1/crawl/MD5 | 89 ++++++++++------------- crawl-2.1.1/crawl/NAMESPACE | 14 +++ crawl-2.1.1/crawl/R/RcppExports.R | 2 crawl-2.1.1/crawl/R/argosDiag2Cov.R | 3 crawl-2.1.1/crawl/R/crawl-package.R | 18 ++-- crawl-2.1.1/crawl/R/crwMLE.R | 42 +++++++--- crawl-2.1.1/crawl/R/crwN2ll.R | 3 crawl-2.1.1/crawl/R/crwPostIS.R | 25 +++--- crawl-2.1.1/crawl/R/crwPredict.R | 29 ++++++- crawl-2.1.1/crawl/R/crwSamplePar.R | 9 ++ crawl-2.1.1/crawl/R/crwSimulator.R | 7 + crawl-2.1.1/crawl/R/displayPar.R | 11 +- crawl-2.1.1/crawl/R/fix_path.R |only crawl-2.1.1/crawl/R/tidy_crwFit.R |only crawl-2.1.1/crawl/man/aic.crw.Rd | 1 crawl-2.1.1/crawl/man/argosDiag2Cov.Rd | 1 crawl-2.1.1/crawl/man/as.flat.Rd | 7 - crawl-2.1.1/crawl/man/beardedSeals.Rd | 1 crawl-2.1.1/crawl/man/check_csv.Rd | 1 crawl-2.1.1/crawl/man/crawl-package.Rd | 15 +-- crawl-2.1.1/crawl/man/crwMLE.Rd | 15 +-- crawl-2.1.1/crawl/man/crwN2ll.Rd | 7 - crawl-2.1.1/crawl/man/crwPostIS.Rd | 7 - crawl-2.1.1/crawl/man/crwPredict.Rd | 14 ++- crawl-2.1.1/crawl/man/crwPredictPlot.Rd | 7 - crawl-2.1.1/crawl/man/crwSamplePar.Rd | 12 +-- crawl-2.1.1/crawl/man/crwSimulator.Rd | 12 +-- crawl-2.1.1/crawl/man/displayPar.Rd | 11 +- crawl-2.1.1/crawl/man/expandPred.Rd | 1 crawl-2.1.1/crawl/man/fillCols.Rd | 1 crawl-2.1.1/crawl/man/fix_path.Rd |only crawl-2.1.1/crawl/man/flatten.Rd | 7 - crawl-2.1.1/crawl/man/get_restricted_segments.Rd |only crawl-2.1.1/crawl/man/harborSeal.Rd | 7 - crawl-2.1.1/crawl/man/intToPOSIX.Rd | 1 crawl-2.1.1/crawl/man/mergeTrackStop.Rd | 1 crawl-2.1.1/crawl/man/northernFurSeal.Rd | 1 crawl-2.1.1/crawl/man/tidy_crwFit.Rd |only crawl-2.1.1/crawl/src/CTCRWN2LL.cpp | 3 crawl-2.1.1/crawl/src/RcppExports.cpp | 82 ++++++++++----------- crawl-2.1.1/crawl/src/SMM_MATS.cpp | 7 + crawl-2.1.1/crawl/src/init.c |only 47 files changed, 276 insertions(+), 221 deletions(-)
Title: Tools for Computation on Batch Systems
Description: As a successor of the packages 'BatchJobs' and 'BatchExperiments',
this package provides a parallel implementation of the Map function for high
performance computing systems managed by schedulers 'IBM Spectrum LSF'
(<http://www-03.ibm.com/systems/spectrum-computing/products/lsf/>),
'OpenLava' (<http://www.openlava.org/>), 'Univa Grid Engine'/'Oracle Grid
Engine' (<http://www.univa.com/>), 'Slurm' (<http://slurm.schedmd.com/>),
'TORQUE/PBS'
(<http://www.adaptivecomputing.com/products/open-source/torque/>), or
'Docker Swarm' (<https://docs.docker.com/swarm/>).
A multicore and socket mode allow the parallelization on a local machines,
and multiple machines can be hooked up via SSH to create a makeshift
cluster. Moreover, the package provides an abstraction mechanism to define
large-scale computer experiments in a well-organized and reproducible way.
Author: Michel Lang [cre, aut],
Bernd Bischl [aut],
Dirk Surmann [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between batchtools versions 0.9.2 dated 2017-02-20 and 0.9.3 dated 2017-04-21
batchtools-0.9.2/batchtools/inst/templates/lsf_simple.tmpl |only batchtools-0.9.2/batchtools/inst/templates/openlava_simple.tmpl |only batchtools-0.9.2/batchtools/inst/templates/sge_simple.tmpl |only batchtools-0.9.2/batchtools/inst/templates/slurm_dortmund.tmpl |only batchtools-0.9.2/batchtools/inst/templates/slurm_simple.tmpl |only batchtools-0.9.2/batchtools/inst/templates/torque_lido.tmpl |only batchtools-0.9.3/batchtools/DESCRIPTION | 6 batchtools-0.9.3/batchtools/MD5 | 134 +++++----- batchtools-0.9.3/batchtools/NEWS.md | 13 batchtools-0.9.3/batchtools/R/Export.R | 2 batchtools-0.9.3/batchtools/R/Hooks.R | 2 batchtools-0.9.3/batchtools/R/JobTables.R | 4 batchtools-0.9.3/batchtools/R/addExperiments.R | 22 - batchtools-0.9.3/batchtools/R/clusterFunctions.R | 24 + batchtools-0.9.3/batchtools/R/clusterFunctionsLSF.R | 3 batchtools-0.9.3/batchtools/R/clusterFunctionsOpenLava.R | 3 batchtools-0.9.3/batchtools/R/clusterFunctionsSGE.R | 3 batchtools-0.9.3/batchtools/R/clusterFunctionsSlurm.R | 3 batchtools-0.9.3/batchtools/R/clusterFunctionsTORQUE.R | 3 batchtools-0.9.3/batchtools/R/config.R | 3 batchtools-0.9.3/batchtools/R/findJobs.R | 22 - batchtools-0.9.3/batchtools/R/getStatus.R | 2 batchtools-0.9.3/batchtools/R/ids.R | 21 - batchtools-0.9.3/batchtools/R/reduceResults.R | 68 ++++- batchtools-0.9.3/batchtools/R/submitJobs.R | 2 batchtools-0.9.3/batchtools/R/sweepRegistry.R | 2 batchtools-0.9.3/batchtools/R/syncRegistry.R | 2 batchtools-0.9.3/batchtools/README.md | 18 + batchtools-0.9.3/batchtools/inst/CITATION | 20 + batchtools-0.9.3/batchtools/inst/doc/v00_Setup.html | 6 batchtools-0.9.3/batchtools/inst/doc/v01_Migration.Rmd | 13 batchtools-0.9.3/batchtools/inst/doc/v01_Migration.html | 18 - batchtools-0.9.3/batchtools/inst/doc/v10_ExamplePiSim.html | 12 batchtools-0.9.3/batchtools/inst/doc/v11_ExampleExperiment.html | 9 batchtools-0.9.3/batchtools/inst/doc/v20_ErrorHandling.html | 19 - batchtools-0.9.3/batchtools/inst/templates/lsf-simple.tmpl |only batchtools-0.9.3/batchtools/inst/templates/openlava-simple.tmpl |only batchtools-0.9.3/batchtools/inst/templates/sge-simple.tmpl |only batchtools-0.9.3/batchtools/inst/templates/slurm-dortmund.tmpl |only batchtools-0.9.3/batchtools/inst/templates/slurm-simple.tmpl |only batchtools-0.9.3/batchtools/inst/templates/torque-lido.tmpl |only batchtools-0.9.3/batchtools/man/JobCollection.Rd | 3 batchtools-0.9.3/batchtools/man/Tags.Rd | 3 batchtools-0.9.3/batchtools/man/addExperiments.Rd | 22 - batchtools-0.9.3/batchtools/man/batchExport.Rd | 2 batchtools-0.9.3/batchtools/man/batchMapResults.Rd | 3 batchtools-0.9.3/batchtools/man/chunkIds.Rd | 3 batchtools-0.9.3/batchtools/man/findJobs.Rd | 7 batchtools-0.9.3/batchtools/man/getErrorMessages.Rd | 3 batchtools-0.9.3/batchtools/man/getJobTable.Rd | 7 batchtools-0.9.3/batchtools/man/getStatus.Rd | 3 batchtools-0.9.3/batchtools/man/grepLogs.Rd | 3 batchtools-0.9.3/batchtools/man/killJobs.Rd | 3 batchtools-0.9.3/batchtools/man/makeClusterFunctionsLSF.Rd | 21 - batchtools-0.9.3/batchtools/man/makeClusterFunctionsOpenLava.Rd | 21 - batchtools-0.9.3/batchtools/man/makeClusterFunctionsSGE.Rd | 21 - batchtools-0.9.3/batchtools/man/makeClusterFunctionsSlurm.Rd | 22 - batchtools-0.9.3/batchtools/man/makeClusterFunctionsTORQUE.Rd | 21 - batchtools-0.9.3/batchtools/man/reduceResults.Rd | 3 batchtools-0.9.3/batchtools/man/reduceResultsList.Rd | 50 +++ batchtools-0.9.3/batchtools/man/removeExperiments.Rd | 3 batchtools-0.9.3/batchtools/man/resetJobs.Rd | 3 batchtools-0.9.3/batchtools/man/runHook.Rd | 2 batchtools-0.9.3/batchtools/man/submitJobs.Rd | 3 batchtools-0.9.3/batchtools/man/summarizeExperiments.Rd | 3 batchtools-0.9.3/batchtools/man/sweepRegistry.Rd | 2 batchtools-0.9.3/batchtools/man/syncRegistry.Rd | 2 batchtools-0.9.3/batchtools/man/waitForJobs.Rd | 3 batchtools-0.9.3/batchtools/tests/testthat/test_ClusterFunctions.R | 8 batchtools-0.9.3/batchtools/tests/testthat/test_ClusterFunctionsSSH.R | 2 batchtools-0.9.3/batchtools/tests/testthat/test_Results.R | 23 + batchtools-0.9.3/batchtools/tests/testthat/test_addAlgorithm.R | 17 + batchtools-0.9.3/batchtools/tests/testthat/test_findJobs.R | 14 - batchtools-0.9.3/batchtools/vignettes/v01_Migration.Rmd | 13 74 files changed, 493 insertions(+), 285 deletions(-)
Title: Sure Independence Screening
Description: Variable selection techniques are essential tools for model
selection and estimation in high-dimensional statistical models. Through this
publicly available package, we provide a unified environment to carry out
variable selection using iterative sure independence screening (SIS) and all
of its variants in generalized linear models and the Cox proportional hazards
model.
Author: Jianqing Fan, Yang Feng, Diego Franco Saldana, Richard Samworth, Yichao
Wu
Maintainer: Yang Feng <yang.feng@columbia.edu>
Diff between SIS versions 0.8-3 dated 2016-10-12 and 0.8-4 dated 2017-04-21
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- R/SIS.R | 41 +++++++++++++++++++++++++---------------- R/predict.SIS.R | 21 ++++----------------- R/subfuns.R | 26 ++++++++++++++++++-------- R/tune.fit.R | 6 +++--- inst/CITATION | 4 +--- man/SIS.Rd | 13 ++++++------- man/predict.SIS.Rd | 24 +++++------------------- man/standardize.Rd | 9 ++++----- man/tune.fit.Rd | 9 ++++----- 11 files changed, 85 insertions(+), 98 deletions(-)
Title: An Enhanced Chart for Simple and Truthful Representation of
Single Observations over Multiple Classes
Description: The sinaplot is a data visualization chart suitable for plotting
any single variable in a multiclass data set. It is an enhanced jitter strip
chart, where the width of the jitter is controlled by the density
distribution of the data within each class.
Author: Nikos Sidiropoulos [aut, cre],
Sina Hadi Sohi [aut],
Nicolas Rapin [aut],
Frederik Otzen Bagger [aut]
Maintainer: Nikos Sidiropoulos <nikos.sidiro@gmail.com>
Diff between sinaplot versions 1.0.0 dated 2016-10-11 and 1.1.0 dated 2017-04-21
DESCRIPTION | 10 - MD5 | 28 +- NAMESPACE | 6 NEWS | 32 +++ R/data.R | 2 R/sinaplot.R | 423 +++++++++++++++++++++++++++++++------------- build/vignette.rds |binary data/blood.rda |binary inst/doc/SinaPlot.R | 24 +- inst/doc/SinaPlot.Rmd | 38 ++- inst/doc/SinaPlot.html | 117 +++++++----- inst/figures/comparison.png |binary man/blood.Rd | 3 man/sinaplot.Rd | 130 ++++++++++--- vignettes/SinaPlot.Rmd | 38 ++- 15 files changed, 601 insertions(+), 250 deletions(-)
Title: Tools for Chromatographic Column Characterization and Modelling
Chromatographic Peak
Description: The quantitative measurement and detection of molecules in HPLC should be carried out by an accurate description of chromatographic peaks. In this package non-linear fitting using a modified Gaussian model with a parabolic variance (PVMG) has been implemented to obtain the retention time and height at the peak maximum. This package also includes the traditional Van Deemter approach and two alternatives approaches to characterize chromatographic column.
Author: Manuel David Peris Diaz, Maria Isabel Alcoriza Balaguer
Maintainer: Manuel David Peris Diaz <madape@alumni.uv.es>
Diff between RpeakChrom versions 0.1.0 dated 2016-12-14 and 1.1.0 dated 2017-04-21
RpeakChrom-0.1.0/RpeakChrom/R/vanDeemterClassic.R |only RpeakChrom-0.1.0/RpeakChrom/man/vanDeemterClassic.Rd |only RpeakChrom-1.1.0/RpeakChrom/DESCRIPTION | 6 RpeakChrom-1.1.0/RpeakChrom/MD5 | 16 RpeakChrom-1.1.0/RpeakChrom/R/processPeak.R | 210 +++---- RpeakChrom-1.1.0/RpeakChrom/R/vanDeemter.R |only RpeakChrom-1.1.0/RpeakChrom/R/vanDeemterAlternative.R | 445 +++++++-------- RpeakChrom-1.1.0/RpeakChrom/man/processPeak.Rd | 90 ++- RpeakChrom-1.1.0/RpeakChrom/man/readChrom.Rd | 35 - RpeakChrom-1.1.0/RpeakChrom/man/vanDeemter.Rd |only RpeakChrom-1.1.0/RpeakChrom/man/vanDeemterAlternative.Rd | 102 ++- 11 files changed, 484 insertions(+), 420 deletions(-)
Title: Precision-Recall and ROC Curves for Weighted and Unweighted Data
Description: Computes the areas under the precision-recall (PR) and ROC curve for weighted (e.g., soft-labeled) and unweighted data. In contrast to other implementations, the interpolation between points of the PR curve is done by a non-linear piecewise function. In addition to the areas under the curves, the curves themselves can also be computed and plotted by a specific S3-method. References: Davis and Goadrich (2006) <doi:10.1145/1143844.1143874>; Keilwagen et al. (2014) <doi:10.1371/journal.pone.0092209>; Grau et al. (2015) <doi:10.1093/bioinformatics/btv153>.
Author: Jan Grau and Jens Keilwagen
Maintainer: Jan Grau <grau@informatik.uni-halle.de>
Diff between PRROC versions 1.1 dated 2015-02-25 and 1.3 dated 2017-04-21
PRROC-1.1/PRROC/inst/tests |only PRROC-1.3/PRROC/DESCRIPTION | 10 PRROC-1.3/PRROC/MD5 | 30 +- PRROC-1.3/PRROC/NAMESPACE | 3 PRROC-1.3/PRROC/R/PRROC.R | 477 +++++++++++++---------------------- PRROC-1.3/PRROC/build/vignette.rds |binary PRROC-1.3/PRROC/inst/CITATION | 17 + PRROC-1.3/PRROC/inst/doc/PRROC.R | 70 ++--- PRROC-1.3/PRROC/inst/doc/PRROC.Rnw | 1 PRROC-1.3/PRROC/inst/doc/PRROC.pdf |binary PRROC-1.3/PRROC/man/PRROC-package.Rd | 8 PRROC-1.3/PRROC/man/pr.curve.Rd | 4 PRROC-1.3/PRROC/man/roc.curve.Rd | 1 PRROC-1.3/PRROC/tests/all_tests.R | 2 PRROC-1.3/PRROC/tests/testthat |only PRROC-1.3/PRROC/vignettes/PRROC.Rnw | 1 16 files changed, 270 insertions(+), 354 deletions(-)
Title: Modelling Microbial Populations
Description: Modelling interacting microbial populations - example applications include human gut microbiota, rumen microbiota and phytoplankton. Solves a system of ordinary differential equations to simulate microbial growth and resource uptake over time.
Author: Helen Kettle [aut, cre]
Maintainer: Helen Kettle <Helen.Kettle@bioss.ac.uk>
Diff between microPop versions 1.1 dated 2017-04-07 and 1.2 dated 2017-04-21
DESCRIPTION | 8 ++-- MD5 | 62 +++++++++++++++++------------------ R/assignNAsToMFGs.R | 13 +++++-- R/combineGrowthLimFuncDefault.R | 5 ++ R/data.R | 2 - R/getKeyRes.R | 25 ++++++-------- R/getNonBoostFrac.R | 16 +++++++-- R/microPopModel.R | 6 +-- R/productionFuncDefault.R | 2 - R/uptakeFuncDefault.R | 6 +-- R/waterUptakeRatio.R | 4 +- build/vignette.rds |binary data/Acetogens.RData |binary data/Bacteroides.RData |binary data/ButyrateProducers3.RData |binary data/LactateProducers.RData |binary data/NoButyFibreDeg.RData |binary data/NoButyStarchDeg.RData |binary data/PropionateProducers.RData |binary data/microbeSysInfo.RData |binary data/resourceSysInfo.RData |binary inst/DemoFiles/rumen.R | 4 +- inst/doc/microPop.pdf |binary inst/extdata/Acetogens.csv | 2 - inst/extdata/Bacteroides.csv | 4 +- inst/extdata/ButyrateProducers3.csv | 2 - inst/extdata/LactateProducers.csv | 2 - inst/extdata/NoButyFibreDeg.csv | 2 - inst/extdata/NoButyStarchDeg.csv | 2 - inst/extdata/PropionateProducers.csv | 4 +- man/MFG.Rd | 2 - man/microPopModel.Rd | 6 +-- 32 files changed, 100 insertions(+), 79 deletions(-)
Title: Using R to Install Stuff (Such As: R, 'Rtools', 'RStudio',
'Git', and More!)
Description: R is great for installing software. Through the 'installr'
package you can automate the updating of R (on Windows, using updateR())
and install new software. Software installation is initiated through a
GUI (just run installr()), or through functions such as: install.Rtools(),
install.pandoc(), install.git(), and many more. The updateR() command
performs the following: finding the latest R version, downloading it,
running the installer, deleting the installation file, copy and updating
old packages to the new R installation.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com),
Barry Rowlingson [ctb],
Boris Hejblum [ctb],
Dason [ctb],
Felix Schonbrodt [ctb],
G. Grothendieck [ctb],
GERGELY DAROCZI [ctb],
Heuristic Andrew [ctb],
James [ctb] (http://stackoverflow.com/users/269476/james),
Thomas Leeper [ctb] (http://thomasleeper.com/),
VitoshKa [ctb],
Yihui Xie [ctb] (http://yihui.name),
Michael Friendly [ctb] (http://datavis.ca/),
Kornelius Rohmeyer [ctb] (http://algorithm-forge.com/techblog/),
Dieter Menne [ctb],
Tyler Hunt [ctb] (https://github.com/JackStat),
Takekatsu Hiramura [ctb] (https://github.com/hiratake55),
Berry Boessenkool [ctb] (https://github.com/BerryBoessenkool),
Jonathan Godfrey [ctb] (https://github.com/ajrgodfrey),
Tom Allard [ctb],
ChingChuan Chen [ctb],
Jonathan Hill [ctb]
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between installr versions 0.18.0 dated 2016-11-05 and 0.19.0 dated 2017-04-21
DESCRIPTION | 22 +-- MD5 | 190 +++++++++++++-------------- NAMESPACE | 2 NEWS | 23 +++ NEWS.md | 23 +++ R/install.R | 44 +++--- R/install.inno.R |only R/updateR.R | 1 R/zzz.R | 3 man/R_version_in_a_folder.Rd | 1 man/add.installr.GUI.Rd | 7 man/add_load_installr_on_startup_menu.Rd | 1 man/add_remove_installr_from_startup_menu.Rd | 1 man/add_to_.First_in_Rprofile.site.Rd | 1 man/ask.user.for.a.row.Rd | 1 man/ask.user.yn.question.Rd | 1 man/barplot_package_users_per_day.Rd | 1 man/browse.latest.R.NEWS.Rd | 1 man/check.for.updates.R.Rd | 1 man/check.integer.Rd | 1 man/checkMD5sums2.Rd | 1 man/copy.packages.between.libraries.Rd | 1 man/cranometer.Rd | 7 man/create.global.library.Rd | 1 man/download_RStudio_CRAN_data.Rd | 1 man/fetch_tag_from_Rd.Rd | 7 man/file.name.from.url.Rd | 1 man/format_RStudio_CRAN_data.Rd | 7 man/freegeoip.Rd | 7 man/get.installed.R.folders.Rd | 1 man/get_Rscript_PID.Rd | 1 man/get_pid.Rd | 1 man/get_tasklist.Rd | 1 man/install.7zip.Rd | 1 man/install.CMake.Rd | 1 man/install.Cygwin.Rd | 3 man/install.FFmpeg.Rd | 1 man/install.GitHub.Rd | 1 man/install.GraphicsMagick.Rd | 1 man/install.ImageMagick.Rd | 1 man/install.LaTeX2RTF.Rd | 1 man/install.LyX.Rd | 1 man/install.MikTeX.Rd | 5 man/install.R.Rd | 1 man/install.RStudio.Rd | 1 man/install.Rdevel.Rd | 1 man/install.Rtools.Rd | 5 man/install.SWFTools.Rd | 1 man/install.Texmaker.Rd | 1 man/install.URL.Rd | 7 man/install.git.Rd | 1 man/install.inno.Rd |only man/install.notepadpp.Rd | 1 man/install.npptor.Rd | 1 man/install.packages.zip.Rd | 1 man/install.pandoc.Rd | 1 man/install.python.Rd | 1 man/installr-package.Rd | 1 man/installr.Rd | 1 man/is.RStudio.Rd | 1 man/is.Rgui.Rd | 1 man/is.empty.Rd | 7 man/is.exe.installed.Rd | 1 man/is.windows.Rd | 1 man/is_in_.First_in_Rprofile.site.Rd | 1 man/kill_all_Rscript_s.Rd | 1 man/kill_pid.Rd | 1 man/kill_process.Rd | 1 man/lineplot_package_downloads.Rd | 7 man/load_installr_on_startup.Rd | 1 man/most_downloaded_packages.Rd | 1 man/myip.Rd | 1 man/os.hibernate.Rd | 7 man/os.lock.Rd | 7 man/os.manage.Rd | 1 man/os.restart.Rd | 7 man/os.shutdown.Rd | 7 man/os.sleep.Rd | 7 man/package_authors.Rd | 1 man/pkgDNLs_worldmapcolor.Rd | 7 man/read_RStudio_CRAN_data.Rd | 7 man/remove.installr.GUI.Rd | 1 man/remove_from_.First_in_Rprofile.site.Rd | 1 man/rename_r_to_R.Rd | 1 man/require2.Rd | 6 man/restart_RGui.Rd | 1 man/rm_installr_from_startup.Rd | 1 man/source.https.Rd | 1 man/system.PATH.Rd | 1 man/turn.number.version.Rd | 1 man/turn.version.to.number.Rd | 1 man/turn.version.to.number1.Rd | 1 man/uninstall.R.Rd | 1 man/uninstall.packages.Rd | 1 man/up_folder.Rd | 1 man/updateR.Rd | 1 man/xlsx2csv.Rd | 1 97 files changed, 242 insertions(+), 258 deletions(-)
Title: Multivariate Adaptive Regression Splines
Description: Build regression models using the techniques in Friedman's
papers "Fast MARS" and "Multivariate Adaptive Regression
Splines". (The term "MARS" is trademarked and thus not used in
the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and
Rob Tibshirani. Uses Alan Miller's Fortran utilities
with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between earth versions 4.4.9.1 dated 2017-03-21 and 4.5.0 dated 2017-04-21
DESCRIPTION | 8 ++--- MD5 | 48 +++++++++++++++--------------- NEWS | 7 +++- R/as.char.R | 4 +- R/lib.R | 4 +- build/partial.rdb |binary inst/doc/earth-notes.pdf |binary inst/doc/earth-varmod.pdf |binary inst/slowtests/earth.times.bat | 2 - inst/slowtests/test.big.bat | 2 - inst/slowtests/test.cv.bat | 2 - inst/slowtests/test.earthc.mak | 2 - inst/slowtests/test.earthmain.gcc.bat | 2 - inst/slowtests/test.earthmain.gcc64.bat | 10 +++--- inst/slowtests/test.full.Rout.save | 6 +-- inst/slowtests/test.full.bat | 2 - inst/slowtests/test.glm.bat | 2 - inst/slowtests/test.incorrect.bat | 2 - inst/slowtests/test.mods.bat | 2 - inst/slowtests/test.plotd.bat | 2 - inst/slowtests/test.pmethod.cv.bat | 2 - inst/slowtests/test.varmod.bat | 2 - inst/slowtests/test.varmod.mgcv.Rout.save | 2 - inst/slowtests/test.varmod.mgcv.bat | 2 - inst/slowtests/test.weights.bat | 2 - 25 files changed, 62 insertions(+), 55 deletions(-)
Title: DMR Detection by Non-Homogeneous Hidden Markov Model from
Methylation Array Data
Description: Perform differential analysis for
methylation array data. Detect differentially
methylated regions (DMRs) from array M-values.
The core is a Non-homogeneous Hidden Markov Model
for estimating spatial correlation and a novel Constrained
Gaussian Mixture Model for modeling the M-value pairs of each individual locus.
Author: Linghao SHEN <sl013@ie.cuhk.edu.hk>
Maintainer: Linghao SHEN <sl013@ie.cuhk.edu.hk>
Diff between DMRMark versions 1.1.0 dated 2017-02-25 and 1.1.1 dated 2017-04-21
DESCRIPTION | 6 MD5 | 10 NAMESPACE | 1 R/DMRViterbi.R | 16 R/FullSampler.R | 1398 +++++++++++++++++++++++++++--------------------------- man/DMRViterbi.Rd | 10 6 files changed, 724 insertions(+), 717 deletions(-)
Title: A Grammar for Turning 'JSON' into Tidy Tables
Description: An easy and consistent way to turn 'JSON' into tidy data frames
that are natural to work with in 'dplyr', 'ggplot2' and other tools.
Author: Jeremy Stanley <jeremy.stanley@gmail.com>
Maintainer: ORPHANED
Diff between tidyjson versions 0.2.1 dated 2015-05-02 and 0.2.2 dated 2017-04-21
tidyjson-0.2.1/tidyjson/tests/test-all.r |only tidyjson-0.2.2/tidyjson/DESCRIPTION | 11 tidyjson-0.2.2/tidyjson/MD5 | 11 tidyjson-0.2.2/tidyjson/NAMESPACE | 1 tidyjson-0.2.2/tidyjson/build/vignette.rds |binary tidyjson-0.2.2/tidyjson/inst/doc/introduction-to-tidyjson.R | 12 tidyjson-0.2.2/tidyjson/inst/doc/introduction-to-tidyjson.html | 1449 +++------- 7 files changed, 569 insertions(+), 915 deletions(-)
Title: Gaussian Linear Models with Linear Covariance Structure
Description: Functions to fit Gaussian linear model by maximising the
residual log likelihood where the covariance structure can be
written as a linear combination of known matrices. Can be used
for multivariate models and random effects models. Easy
straight forward manner to specify random effects models,
including random interactions. Code now optimised to use
Sherman Morrison Woodbury identities for matrix inversion in
random effects models. We've added the ability to fit models
using any kernel as well as a function to return the mean and
covariance of random effects conditional on the data (BLUPs).
Author: David Clifford and Peter McCullagh. Additional contributions by
HJ Auinger.
Maintainer: ORPHANED
Diff between regress versions 1.3-14 dated 2014-07-14 and 1.3-15 dated 2017-04-21
regress-1.3-14/regress/tests/OLS.r |only regress-1.3-14/regress/tests/predictionVariance.r |only regress-1.3-15/regress/DESCRIPTION | 13 ++++++++----- regress-1.3-15/regress/MD5 | 6 ++---- regress-1.3-15/regress/NAMESPACE | 7 +++++++ 5 files changed, 17 insertions(+), 9 deletions(-)
Title: Tools for Partial Least Squares Path Modeling (PLS-PM)
Description: Partial Least Squares Path Modeling (PLS-PM)
analysis for both metric and
non-metric data, as well as REBUS analysis.
Author: Gaston Sanchez [aut, cre],
Laura Trinchera [aut],
Giorgio Russolillo [aut]
Maintainer: ORPHANED
Diff between plspm versions 0.4.7 dated 2015-05-25 and 0.4.8 dated 2017-04-21
plspm-0.4.7/plspm/tests |only plspm-0.4.8/plspm/DESCRIPTION | 11 +++++++---- plspm-0.4.8/plspm/MD5 | 9 ++++----- plspm-0.4.8/plspm/NAMESPACE | 5 +++++ plspm-0.4.8/plspm/build/vignette.rds |binary plspm-0.4.8/plspm/inst/doc/plspm_introduction.pdf |binary 6 files changed, 16 insertions(+), 9 deletions(-)
Title: Evaluation Metrics for Machine Learning
Description: Metrics is a set of evaluation metrics that is commonly
used in supervised machine learning.
Author: Ben Hamner <ben@benhamner.com>
Maintainer: ORPHANED
Diff between Metrics versions 0.1.1 dated 2012-06-20 and 0.1.2 dated 2017-04-21
Metrics-0.1.1/Metrics/run_tests.sh |only Metrics-0.1.1/Metrics/tests/test_all.r |only Metrics-0.1.2/Metrics/DESCRIPTION | 15 ++++++++++----- Metrics-0.1.2/Metrics/MD5 | 5 ++--- Metrics-0.1.2/Metrics/tests/test_all.R |only 5 files changed, 12 insertions(+), 8 deletions(-)
Title: Framework for the Analysis of Genomic Prediction Data using R
Description: A collection of functions required for genomic prediction which were developed within the Synbreed project for synergistic plant and animal breeding (<http://www.synbreed.tum.de>). This covers data processing, data visualization, and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats in plant and animal breeding. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Hans-Juergen Auinger, Valentin Wimmer, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Maintainer: Hans-Juergen Auinger <auinger@tum.de>
Diff between synbreed versions 0.12-5 dated 2017-04-20 and 0.12-6 dated 2017-04-21
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- NEWS | 7 +++++++ R/codeGeno.r | 5 +---- vignettes/figs/cattleHist.pdf |binary vignettes/figs/genMapCattle.pdf |binary vignettes/figs/genMapMaize.pdf |binary vignettes/figs/genMapMice.pdf |binary vignettes/figs/maizeHist.pdf |binary vignettes/figs/miceHist.pdf |binary 10 files changed, 23 insertions(+), 19 deletions(-)
Title: Recursive Partitioning and Regression Trees
Description: Recursive partitioning for classification,
regression and survival trees. An implementation of most of the
functionality of the 1984 book by Breiman, Friedman, Olshen and Stone.
Author: Terry Therneau [aut],
Beth Atkinson [aut],
Brian Ripley [aut, trl, cre] (author of initial R port)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between rpart versions 4.1-10 dated 2015-06-29 and 4.1-11 dated 2017-04-21
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- build/vignette.rds |binary inst/doc/longintro.pdf |binary inst/doc/usercode.pdf |binary man/rpart.Rd | 2 +- src/rpart.h | 3 +++ src/rpart_callback.c | 2 ++ tests/Examples/rpart-Ex.Rout.save | 12 ++++++------ 10 files changed, 28 insertions(+), 20 deletions(-)
Title: Confidence Intervals for Comparisons of Binomial or Poisson
Rates
Description: Computes confidence intervals for the rate (or risk)
difference ("RD") or rate ratio (or relative risk, "RR") for
binomial proportions or Poisson rates, or for odds ratio
("OR", binomial only). Also confidence intervals for a single
binomial or Poisson rate, and intervals for matched pairs.
Includes asymptotic score methods including skewness corrections,
which have been developed in Laud (2017, in press)
from Miettinen & Nurminen (1985) <doi:10.1002/sim.4780040211> and
Gart & Nam (1988) <doi:10.2307/2531848>. Also includes MOVER methods
(Method Of Variance Estimates Recovery), derived from the
Newcombe method but using equal-tailed Jeffreys intervals,
and generalised for incorporating prior information.
Also methods for stratified calculations (e.g. meta-analysis),
either assuming fixed effects or incorporating stratum
heterogeneity.
Author: Pete Laud [aut, cre]
Maintainer: Pete Laud <p.j.laud@sheffield.ac.uk>
Diff between ratesci versions 0.1-0 dated 2016-11-12 and 0.2-0 dated 2017-04-21
DESCRIPTION | 28 ++-- MD5 | 32 ++-- NAMESPACE | 2 NEWS.md | 18 ++ R/moverci.R | 101 +++++++++------ R/pairbinci.R |only R/ratesci-package.R | 2 R/scoreci.R | 295 ++++++++++++++++++++++++++++---------------- man/jeffreysci.Rd | 7 - man/moverbci.Rd | 4 man/moverci.Rd | 8 - man/pairbinci.Rd |only man/ratesci-package.Rd | 2 man/scasci.Rd | 14 +- man/scoreci.Rd | 22 ++- man/tdasci.Rd | 13 + tests/testthat/Table2.Rdata |only tests/testthat/test3.R | 39 ++++- tests/testthat/test4.R |only 19 files changed, 377 insertions(+), 210 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley,
"Modern Applied Statistics with S" (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Kurt Hornik [trl] (partial port ca 1998),
Albrecht Gebhardt [trl] (partial port ca 1998),
David Firth [ctb]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between MASS versions 7.3-45 dated 2015-11-10 and 7.3-47 dated 2017-04-21
DESCRIPTION | 11 ++++++----- MD5 | 12 ++++++------ R/rlm.R | 4 ++-- man/width.SJ.Rd | 7 ++++++- src/MASS.c | 29 ++++++++++++++++------------- src/lqs.c | 10 ++++------ tests/Examples/MASS-Ex.Rout.save | 11 ++++------- 7 files changed, 44 insertions(+), 40 deletions(-)
Title: Simply Create LaTeX and HTML Tables
Description: Creates HTML and LaTeX tables. Provides similar
functionality to 'xtable', but does more, with a simpler interface.
Author: David Hugh-Jones
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between huxtable versions 0.1.1 dated 2017-03-14 and 0.2.0 dated 2017-04-21
huxtable-0.1.1/huxtable/inst/doc/introduction-to-huxtable.R |only huxtable-0.1.1/huxtable/inst/doc/introduction-to-huxtable.Rmd |only huxtable-0.1.1/huxtable/inst/doc/introduction-to-huxtable.html |only huxtable-0.1.1/huxtable/man/bottom_border.Rd |only huxtable-0.1.1/huxtable/man/right_border.Rd |only huxtable-0.1.1/huxtable/man/set_all_padding.Rd |only huxtable-0.1.1/huxtable/man/top_border.Rd |only huxtable-0.1.1/huxtable/vignettes/introduction-to-huxtable.Rmd |only huxtable-0.2.0/huxtable/DESCRIPTION | 11 huxtable-0.2.0/huxtable/MD5 | 168 - huxtable-0.2.0/huxtable/NAMESPACE | 203 - huxtable-0.2.0/huxtable/NEWS.md | 22 huxtable-0.2.0/huxtable/R/FlexTable.R |only huxtable-0.2.0/huxtable/R/HTML.R | 72 huxtable-0.2.0/huxtable/R/LaTeX.R | 208 - huxtable-0.2.0/huxtable/R/attributes.R | 625 +++- huxtable-0.2.0/huxtable/R/huxreg.R |only huxtable-0.2.0/huxtable/R/huxtable.R | 514 ++- huxtable-0.2.0/huxtable/R/row-col-fns.R |only huxtable-0.2.0/huxtable/R/screen.R | 198 + huxtable-0.2.0/huxtable/R/themes.R | 39 huxtable-0.2.0/huxtable/R/utils.R |only huxtable-0.2.0/huxtable/README.md | 26 huxtable-0.2.0/huxtable/build/vignette.rds |binary huxtable-0.2.0/huxtable/inst/doc/design-principles.R | 8 huxtable-0.2.0/huxtable/inst/doc/design-principles.Rmd | 23 huxtable-0.2.0/huxtable/inst/doc/design-principles.html | 1400 +++++----- huxtable-0.2.0/huxtable/inst/doc/huxreg.R |only huxtable-0.2.0/huxtable/inst/doc/huxreg.Rmd |only huxtable-0.2.0/huxtable/inst/doc/huxreg.html |only huxtable-0.2.0/huxtable/inst/doc/huxtable.R |only huxtable-0.2.0/huxtable/inst/doc/huxtable.Rmd |only huxtable-0.2.0/huxtable/inst/doc/huxtable.html |only huxtable-0.2.0/huxtable/man/add_colnames.Rd | 2 huxtable-0.2.0/huxtable/man/add_footnote.Rd |only huxtable-0.2.0/huxtable/man/align.Rd | 20 huxtable-0.2.0/huxtable/man/as_FlexTable.Rd |only huxtable-0.2.0/huxtable/man/background_color.Rd | 22 huxtable-0.2.0/huxtable/man/bold.Rd | 24 huxtable-0.2.0/huxtable/man/caption.Rd | 7 huxtable-0.2.0/huxtable/man/caption_pos.Rd | 2 huxtable-0.2.0/huxtable/man/cbind.huxtable.Rd | 14 huxtable-0.2.0/huxtable/man/col_width.Rd | 9 huxtable-0.2.0/huxtable/man/colspan.Rd | 10 huxtable-0.2.0/huxtable/man/dplyr-verbs.Rd |only huxtable-0.2.0/huxtable/man/escape_contents.Rd | 23 huxtable-0.2.0/huxtable/man/every.Rd |only huxtable-0.2.0/huxtable/man/extract-methods.Rd | 14 huxtable-0.2.0/huxtable/man/final.Rd |only huxtable-0.2.0/huxtable/man/font.Rd | 20 huxtable-0.2.0/huxtable/man/font_size.Rd | 20 huxtable-0.2.0/huxtable/man/guess_knitr_output_format.Rd |only huxtable-0.2.0/huxtable/man/height.Rd | 2 huxtable-0.2.0/huxtable/man/hux_logo.Rd | 6 huxtable-0.2.0/huxtable/man/huxreg.Rd |only huxtable-0.2.0/huxtable/man/huxtable-package.Rd | 13 huxtable-0.2.0/huxtable/man/huxtable.Rd | 2 huxtable-0.2.0/huxtable/man/is_a_number.Rd |only huxtable-0.2.0/huxtable/man/label.Rd | 2 huxtable-0.2.0/huxtable/man/left_border.Rd | 57 huxtable-0.2.0/huxtable/man/left_border_color.Rd |only huxtable-0.2.0/huxtable/man/left_padding.Rd | 42 huxtable-0.2.0/huxtable/man/na_string.Rd | 23 huxtable-0.2.0/huxtable/man/number_format.Rd | 20 huxtable-0.2.0/huxtable/man/pad_decimal.Rd |only huxtable-0.2.0/huxtable/man/position.Rd | 2 huxtable-0.2.0/huxtable/man/print.huxtable.Rd |only huxtable-0.2.0/huxtable/man/report_latex_dependencies.Rd | 9 huxtable-0.2.0/huxtable/man/rotation.Rd | 26 huxtable-0.2.0/huxtable/man/row_height.Rd | 4 huxtable-0.2.0/huxtable/man/rowspan.Rd | 10 huxtable-0.2.0/huxtable/man/rowspecs.Rd |only huxtable-0.2.0/huxtable/man/set_all_border_colors.Rd |only huxtable-0.2.0/huxtable/man/set_all_borders.Rd | 18 huxtable-0.2.0/huxtable/man/set_cell_properties.Rd |only huxtable-0.2.0/huxtable/man/t.huxtable.Rd | 4 huxtable-0.2.0/huxtable/man/tabular_environment.Rd | 2 huxtable-0.2.0/huxtable/man/text_color.Rd | 22 huxtable-0.2.0/huxtable/man/themes.Rd | 8 huxtable-0.2.0/huxtable/man/to_html.Rd | 10 huxtable-0.2.0/huxtable/man/to_latex.Rd | 4 huxtable-0.2.0/huxtable/man/to_md.Rd | 4 huxtable-0.2.0/huxtable/man/to_screen.Rd | 15 huxtable-0.2.0/huxtable/man/valign.Rd | 24 huxtable-0.2.0/huxtable/man/where.Rd |only huxtable-0.2.0/huxtable/man/width.Rd | 2 huxtable-0.2.0/huxtable/man/wrap.Rd | 22 huxtable-0.2.0/huxtable/tests/testthat.R | 1 huxtable-0.2.0/huxtable/tests/testthat/functions.R | 20 huxtable-0.2.0/huxtable/tests/testthat/guess-output-format-test-Rmd-html.Rmd |only huxtable-0.2.0/huxtable/tests/testthat/guess-output-format-test-Rmd-pdf.Rmd |only huxtable-0.2.0/huxtable/tests/testthat/guess-output-format-test.Rhtml |only huxtable-0.2.0/huxtable/tests/testthat/guess-output-format-test.Rnw |only huxtable-0.2.0/huxtable/tests/testthat/multirow.rds |binary huxtable-0.2.0/huxtable/tests/testthat/test-FlexTable.R |only huxtable-0.2.0/huxtable/tests/testthat/test-attributes.R | 45 huxtable-0.2.0/huxtable/tests/testthat/test-dplyr.R |only huxtable-0.2.0/huxtable/tests/testthat/test-huxreg.R |only huxtable-0.2.0/huxtable/tests/testthat/test-object-manipulation.R | 163 + huxtable-0.2.0/huxtable/tests/testthat/test-output.R | 84 huxtable-0.2.0/huxtable/tests/testthat/test-set-interface.R |only huxtable-0.2.0/huxtable/tests/testthat/test-themes.R |only huxtable-0.2.0/huxtable/tests/testthat/test-with-pandoc.R |only huxtable-0.2.0/huxtable/vignettes/comparison.csv | 75 huxtable-0.2.0/huxtable/vignettes/design-principles.Rmd | 23 huxtable-0.2.0/huxtable/vignettes/huxreg.Rmd |only huxtable-0.2.0/huxtable/vignettes/huxtable.Rmd |only huxtable-0.2.0/huxtable/vignettes/placeins-header.tex |only 108 files changed, 2928 insertions(+), 1540 deletions(-)
Title: Bootstrap Functions (Originally by Angelo Canty for S)
Description: Functions and datasets for bootstrapping from the
book "Bootstrap Methods and Their Application" by A. C. Davison and
D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.
Author: Angelo Canty [aut],
Brian Ripley [aut, trl, cre] (author of parallel support)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between boot versions 1.3-18 dated 2016-02-23 and 1.3-19 dated 2017-04-21
ChangeLog | 8 +++ DESCRIPTION | 8 +-- MD5 | 6 +- tests/Examples/boot-Ex.Rout.save | 94 +++++++++++++++++++-------------------- 4 files changed, 62 insertions(+), 54 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-06-24 0.2.3
2014-03-31 0.2
2013-05-25 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-01-31 0.1-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-31 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-05-13 1.3.0
2015-02-11 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-12-07 0.6.2
2015-10-08 0.6.1
2015-07-01 0.6
2014-09-16 0.4.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-02-16 2.4.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-27 0.2
2014-10-30 0.1
Title: Kernel-Smoothed Nonparametric Methods for Environmental Exposure
Data Subject to Detection Limits
Description: Calculate the kernel-smoothed nonparametric estimator for the exposure distribution in presence of detection limits.
Author: Yuchen Yang <yuchen.y@uky.edu>, Li Chen <lichenuky@uky.edu>
Maintainer: Yuchen Yang <yuchen.y@uky.edu>
Diff between KENDL versions 1.0 dated 2017-03-21 and 1.1 dated 2017-04-21
DESCRIPTION | 6 +- MD5 | 6 +- man/KRKM.Rd | 147 ++++++++++++++++++++++++++++--------------------------- man/plot.KRKM.Rd | 104 +++++++++++++++++++------------------- 4 files changed, 135 insertions(+), 128 deletions(-)
Title: Fixed Rank Kriging
Description: Fixed Rank Kriging is a tool for spatial/spatio-temporal modelling
and prediction with large datasets. The approach, discussed in Cressie and
Johannesson (2008) <DOI:10.1111/j.1467-9868.2007.00633.x>, decomposes the field,
and hence the covariance function, using a fixed set of n basis functions,
where n is typically much smaller than the number of data points (or polygons) m.
The method naturally allows for non-stationary, anisotropic covariance functions
and the use of observations with varying support (with known error variance). The
projected field is a key building block of the Spatial Random Effects (SRE) model,
on which this package is based. The package FRK provides helper functions to model,
fit, and predict using an SRE with relative ease.
Author: Andrew Zammit-Mangion [aut, cre],
Timothy Davis [ctb],
Patrick Amestoy [ctb],
Iain Duff [ctb],
John K. Reid [ctb]
Maintainer: Andrew Zammit-Mangion <andrewzm@gmail.com>
Diff between FRK versions 0.1.1 dated 2017-03-07 and 0.1.2 dated 2017-04-21
FRK-0.1.1/FRK/R/dates.R |only FRK-0.1.1/FRK/man/Basisclass.Rd |only FRK-0.1.1/FRK/man/sp_to_ST_basis.Rd |only FRK-0.1.1/FRK/man/timeline.Rd |only FRK-0.1.1/FRK/vignettes/FRK_Section1.tex |only FRK-0.1.1/FRK/vignettes/FRK_Section7.tex |only FRK-0.1.2/FRK/DESCRIPTION | 44 FRK-0.1.2/FRK/LICENSE.note | 18 FRK-0.1.2/FRK/MD5 | 177 - FRK-0.1.2/FRK/NAMESPACE | 19 FRK-0.1.2/FRK/R/AllClass.R | 75 FRK-0.1.2/FRK/R/AllGeneric.R | 93 FRK-0.1.2/FRK/R/FRK.R | 7 FRK-0.1.2/FRK/R/FRK_wrapper.R | 199 - FRK-0.1.2/FRK/R/SREutils.R | 1937 ++++++------- FRK-0.1.2/FRK/R/basisfns.R | 777 +++-- FRK-0.1.2/FRK/R/datadoc.R | 148 - FRK-0.1.2/FRK/R/geometryfns.R | 2342 ++++++++-------- FRK-0.1.2/FRK/R/linalgfns.R | 218 - FRK-0.1.2/FRK/R/options.R | 81 FRK-0.1.2/FRK/R/plottingfns.R | 188 - FRK-0.1.2/FRK/R/zzz.R |only FRK-0.1.2/FRK/build/vignette.rds |binary FRK-0.1.2/FRK/data/AIRS_05_2003.rda |binary FRK-0.1.2/FRK/data/NOAA_df_1990.rda |binary FRK-0.1.2/FRK/data/isea3h.rda |binary FRK-0.1.2/FRK/data/worldmap.rda |binary FRK-0.1.2/FRK/inst/doc/FRK_intro.R | 67 FRK-0.1.2/FRK/inst/doc/FRK_intro.Rnw |only FRK-0.1.2/FRK/inst/doc/FRK_intro.pdf |binary FRK-0.1.2/FRK/man/AIRS_05_2003.Rd | 11 FRK-0.1.2/FRK/man/Basis-class.Rd |only FRK-0.1.2/FRK/man/Basis_data.frame.Rd |only FRK-0.1.2/FRK/man/FRK-package.Rd | 3 FRK-0.1.2/FRK/man/NOAA_df_1990.Rd | 14 FRK-0.1.2/FRK/man/SRE-class.Rd | 30 FRK-0.1.2/FRK/man/SRE.Rd | 102 FRK-0.1.2/FRK/man/STplane.Rd | 1 FRK-0.1.2/FRK/man/STsphere.Rd | 3 FRK-0.1.2/FRK/man/SpatialPolygonsDataFrame_to_df.Rd | 5 FRK-0.1.2/FRK/man/TensorP.Rd | 5 FRK-0.1.2/FRK/man/auto_BAUs.Rd | 33 FRK-0.1.2/FRK/man/auto_basis.Rd | 23 FRK-0.1.2/FRK/man/df_to_SpatialPolygons.Rd | 5 FRK-0.1.2/FRK/man/dist-matrix.Rd | 1 FRK-0.1.2/FRK/man/distance.Rd | 3 FRK-0.1.2/FRK/man/distances.Rd | 7 FRK-0.1.2/FRK/man/draw_world.Rd | 9 FRK-0.1.2/FRK/man/eval_basis.Rd | 49 FRK-0.1.2/FRK/man/initialize-manifold-method.Rd | 1 FRK-0.1.2/FRK/man/isea3h.Rd | 13 FRK-0.1.2/FRK/man/local_basis.Rd | 17 FRK-0.1.2/FRK/man/manifold-class.Rd | 15 FRK-0.1.2/FRK/man/manifold.Rd | 1 FRK-0.1.2/FRK/man/measure-class.Rd | 6 FRK-0.1.2/FRK/man/nbasis.Rd | 7 FRK-0.1.2/FRK/man/nres.Rd | 9 FRK-0.1.2/FRK/man/opts_FRK.Rd | 5 FRK-0.1.2/FRK/man/plane.Rd | 3 FRK-0.1.2/FRK/man/plotting-themes.Rd | 5 FRK-0.1.2/FRK/man/real_line.Rd | 1 FRK-0.1.2/FRK/man/show_basis.Rd | 9 FRK-0.1.2/FRK/man/sphere.Rd | 1 FRK-0.1.2/FRK/man/type.Rd | 1 FRK-0.1.2/FRK/man/worldmap.Rd | 9 FRK-0.1.2/FRK/src/FRK-init.c |only FRK-0.1.2/FRK/src/FRK-win.def |only FRK-0.1.2/FRK/src/amd.h | 2 FRK-0.1.2/FRK/src/amd_1.c | 2 FRK-0.1.2/FRK/src/amd_2.c | 2 FRK-0.1.2/FRK/src/amd_aat.c | 2 FRK-0.1.2/FRK/src/amd_control.c | 2 FRK-0.1.2/FRK/src/amd_defaults.c | 2 FRK-0.1.2/FRK/src/amd_dump.c | 2 FRK-0.1.2/FRK/src/amd_global.c | 2 FRK-0.1.2/FRK/src/amd_info.c | 2 FRK-0.1.2/FRK/src/amd_internal.h | 2 FRK-0.1.2/FRK/src/amd_order.c | 2 FRK-0.1.2/FRK/src/amd_order_wrapper.h |only FRK-0.1.2/FRK/src/amd_post_tree.c | 2 FRK-0.1.2/FRK/src/amd_postorder.c | 2 FRK-0.1.2/FRK/src/amd_preprocess.c | 2 FRK-0.1.2/FRK/src/amd_valid.c | 2 FRK-0.1.2/FRK/src/distR.h |only FRK-0.1.2/FRK/tests/testthat/Rplots.pdf |binary FRK-0.1.2/FRK/tests/testthat/test_BAUs.R | 83 FRK-0.1.2/FRK/tests/testthat/test_SRE.R | 7 FRK-0.1.2/FRK/tests/testthat/test_basis.R | 229 - FRK-0.1.2/FRK/tests/testthat/test_domains.R | 1 FRK-0.1.2/FRK/tests/testthat/test_linalg.R | 50 FRK-0.1.2/FRK/tests/testthat/test_other.R | 29 FRK-0.1.2/FRK/tests/testthat/test_sre_polygon_predict.R | 8 FRK-0.1.2/FRK/tests/testthat/test_support.R | 4 FRK-0.1.2/FRK/tests/testthat/test_wrapper.R | 4 FRK-0.1.2/FRK/vignettes/FRK_Sections_21_23.tex | 157 - FRK-0.1.2/FRK/vignettes/FRK_bib.bib | 91 FRK-0.1.2/FRK/vignettes/FRK_intro.Rnw |only 97 files changed, 4087 insertions(+), 3403 deletions(-)
Title: Venn Diagrams in 2D and 3D
Description: Calculate and plot Venn diagrams in 2D and 3D.
Author: Zehao Xu [aut, cre],
R. Wayne Oldford [ctb],
Martin Lysy [ctb]
Maintainer: Zehao Xu <z267xu@uwaterloo.ca>
Diff between vennplot versions 0.9.01 dated 2017-04-14 and 0.9.02 dated 2017-04-21
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/vennplot.R | 2 -- man/vennplot.Rd | 1 - 4 files changed, 7 insertions(+), 10 deletions(-)
Title: Unix System Utilities
Description: Bindings to system utilities found in most Unix systems such as
POSIX functions which are not part of the Standard C Library.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between unix versions 1.0 dated 2017-04-03 and 1.3 dated 2017-04-21
DESCRIPTION | 11 ++++++----- MD5 | 23 +++++++++++++---------- NAMESPACE | 13 +++++++++++-- NEWS |only R/process.R | 42 ++++++++++++++++++++++++++++++++++++++---- R/rlimit.R | 44 ++++++++++++++++++++++++++++++++++++++------ man/process.Rd | 30 ++++++++++++++++++++++++------ man/rlimit.Rd | 21 +++++++++++++++++---- src/chroot.c | 13 ++++++++++++- src/process.c | 18 ++++++++++++++++++ src/rlimit.c | 27 +++++++++++++++++++++------ src/userinfo.c | 6 +----- tests |only 13 files changed, 199 insertions(+), 49 deletions(-)
Title: Interface to Species Occurrence Data Sources
Description: A programmatic interface to many species occurrence data sources,
including Global Biodiversity Information Facility ('GBIF'), 'USGSs'
Biodiversity Information Serving Our Nation ('BISON'), 'iNaturalist',
Berkeley 'Ecoinformatics' Engine, 'eBird', 'AntWeb', Integrated Digitized
'Biocollections' ('iDigBio'), 'VertNet', Ocean 'Biogeographic' Information
System ('OBIS'), and Atlas of Living Australia ('ALA'). Includes
functionality for retrieving species occurrence data, and combining
those data.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [ctb],
Ted Hart [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between spocc versions 0.6.0 dated 2016-12-07 and 0.7.0 dated 2017-04-21
spocc-0.6.0/spocc/R/on_load.R |only spocc-0.6.0/spocc/R/read_wkt.R |only spocc-0.6.0/spocc/inst/js |only spocc-0.6.0/spocc/man/wkt.Rd |only spocc-0.7.0/spocc/DESCRIPTION | 21 +-- spocc-0.7.0/spocc/LICENSE | 2 spocc-0.7.0/spocc/MD5 | 138 +++++++++----------- spocc-0.7.0/spocc/NAMESPACE | 7 - spocc-0.7.0/spocc/NEWS.md | 29 ++++ spocc-0.7.0/spocc/R/ala_helpers.R | 29 ++-- spocc-0.7.0/spocc/R/antweb_helpers.R | 56 +++++--- spocc-0.7.0/spocc/R/as.ala.R | 31 ++-- spocc-0.7.0/spocc/R/as.antweb.R | 38 +++-- spocc-0.7.0/spocc/R/as.bison.R | 46 +++--- spocc-0.7.0/spocc/R/as.ecoengine.R | 48 +++---- spocc-0.7.0/spocc/R/as.gbif.R | 42 +++--- spocc-0.7.0/spocc/R/as.idigbio.R | 39 ++--- spocc-0.7.0/spocc/R/as.inat.R | 44 +++--- spocc-0.7.0/spocc/R/as.obis.R | 31 ++-- spocc-0.7.0/spocc/R/as.vertnet.R | 11 - spocc-0.7.0/spocc/R/ecoengine_helpers.R | 105 ++++++++++----- spocc-0.7.0/spocc/R/fixnames.r | 34 ++--- spocc-0.7.0/spocc/R/handle_sp.R | 33 +--- spocc-0.7.0/spocc/R/inat.R | 85 ++++++++---- spocc-0.7.0/spocc/R/inspect.R | 19 +- spocc-0.7.0/spocc/R/methods.r | 31 +++- spocc-0.7.0/spocc/R/obis_helpers.R | 28 ++-- spocc-0.7.0/spocc/R/occ.r | 42 ++++-- spocc-0.7.0/spocc/R/occ2df.R | 46 +++--- spocc-0.7.0/spocc/R/occ_coverage.R | 8 - spocc-0.7.0/spocc/R/occ_names.R | 67 +++++----- spocc-0.7.0/spocc/R/occ_names_options.R | 51 ++++--- spocc-0.7.0/spocc/R/occ_options.r | 60 +++++---- spocc-0.7.0/spocc/R/plugin_helpers.R | 20 +-- spocc-0.7.0/spocc/R/plugins.r | 124 ++++++++++++------ spocc-0.7.0/spocc/R/spocc-package.R | 43 +++--- spocc-0.7.0/spocc/R/spocc_duplicates.R | 38 +++-- spocc-0.7.0/spocc/R/wkt_bbox.R | 79 ++++------- spocc-0.7.0/spocc/R/wkt_vis.r | 49 ++----- spocc-0.7.0/spocc/R/zzz.r | 24 ++- spocc-0.7.0/spocc/README.md | 66 ++++----- spocc-0.7.0/spocc/build/vignette.rds |binary spocc-0.7.0/spocc/inst/doc/spocc_vignette.Rmd | 166 ++++++++++++------------- spocc-0.7.0/spocc/inst/doc/spocc_vignette.html | 166 ++++++++++++------------- spocc-0.7.0/spocc/man/as.ala.Rd | 7 - spocc-0.7.0/spocc/man/as.antweb.Rd | 9 - spocc-0.7.0/spocc/man/as.bison.Rd | 19 +- spocc-0.7.0/spocc/man/as.ecoengine.Rd | 13 + spocc-0.7.0/spocc/man/as.gbif.Rd | 17 +- spocc-0.7.0/spocc/man/as.idigbio.Rd | 15 +- spocc-0.7.0/spocc/man/as.inat.Rd | 15 +- spocc-0.7.0/spocc/man/as.obis.Rd | 9 - spocc-0.7.0/spocc/man/as.vertnet.Rd | 12 - spocc-0.7.0/spocc/man/bbox2wkt.Rd | 40 ++++-- spocc-0.7.0/spocc/man/fixnames.Rd | 28 ++-- spocc-0.7.0/spocc/man/inspect.Rd | 18 +- spocc-0.7.0/spocc/man/occ.Rd | 5 spocc-0.7.0/spocc/man/occ2df.Rd | 33 ++-- spocc-0.7.0/spocc/man/occ_coverage.Rd | 7 - spocc-0.7.0/spocc/man/occ_names.Rd | 49 +++---- spocc-0.7.0/spocc/man/occ_names_options.Rd | 28 ++-- spocc-0.7.0/spocc/man/occ_options.Rd | 40 +++--- spocc-0.7.0/spocc/man/spocc-package.Rd | 33 ++-- spocc-0.7.0/spocc/man/spocc_capwords.Rd | 10 - spocc-0.7.0/spocc/man/spocc_duplicates.Rd | 39 +++-- spocc-0.7.0/spocc/man/spocc_objects.Rd | 5 spocc-0.7.0/spocc/man/wkt_vis.Rd | 5 spocc-0.7.0/spocc/tests/testthat/test-occ.R | 4 spocc-0.7.0/spocc/tests/testthat/test-occ2df.R | 2 spocc-0.7.0/spocc/vignettes/spocc_vignette.Rmd | 166 ++++++++++++------------- 70 files changed, 1425 insertions(+), 1199 deletions(-)
Title: The R Genome Browser
Description: Classes and methods to efficiently handle (slice, annotate, draw ...) genomic features (such as genes or transcripts), and an interactive interface to browse them.
Author: Sylvain Mareschal
Maintainer: Sylvain Mareschal <maressyl@gmail.com>
Diff between Rgb versions 1.5.0 dated 2017-03-03 and 1.5.1 dated 2017-04-21
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/draw.hist.R | 2 +- R/tk.browse.R | 24 ++++++++++++++++-------- inst/NEWS.Rd | 7 +++++++ inst/doc/Howto.pdf |binary man/draw.hist.Rd | 2 +- 7 files changed, 35 insertions(+), 20 deletions(-)
Title: 'Rcpp' Bindings for the 'CCTZ' Library
Description: 'Rcpp' Access to the 'CCTZ' timezone library is provided. 'CCTZ' is
a C++ library for translating between absolute and civil times using the rules
of a time zone. The 'CCTZ' source code, released under the Apache 2.0 License,
is included in this package. See <https://github.com/google/cctz> for more
details.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppCCTZ versions 0.2.1 dated 2017-02-04 and 0.2.2 dated 2017-04-21
RcppCCTZ-0.2.1/RcppCCTZ/inst/include/src |only RcppCCTZ-0.2.2/RcppCCTZ/ChangeLog | 41 RcppCCTZ-0.2.2/RcppCCTZ/DESCRIPTION | 10 RcppCCTZ-0.2.2/RcppCCTZ/MD5 | 44 RcppCCTZ-0.2.2/RcppCCTZ/NAMESPACE | 2 RcppCCTZ-0.2.2/RcppCCTZ/inst/NEWS.Rd | 7 RcppCCTZ-0.2.2/RcppCCTZ/inst/include/civil_time_detail.h | 212 ++-- RcppCCTZ-0.2.2/RcppCCTZ/inst/include/time_zone.h | 68 - RcppCCTZ-0.2.2/RcppCCTZ/inst/include/time_zone_fixed.h |only RcppCCTZ-0.2.2/RcppCCTZ/inst/include/time_zone_if.h | 5 RcppCCTZ-0.2.2/RcppCCTZ/inst/include/time_zone_impl.h | 5 RcppCCTZ-0.2.2/RcppCCTZ/inst/include/time_zone_info.h | 96 -- RcppCCTZ-0.2.2/RcppCCTZ/inst/include/time_zone_libc.h | 10 RcppCCTZ-0.2.2/RcppCCTZ/inst/include/time_zone_posix.h | 16 RcppCCTZ-0.2.2/RcppCCTZ/inst/include/zone_info_source.h |only RcppCCTZ-0.2.2/RcppCCTZ/src/civil_time_detail.cc |only RcppCCTZ-0.2.2/RcppCCTZ/src/init.c |only RcppCCTZ-0.2.2/RcppCCTZ/src/time_tool.cc | 62 - RcppCCTZ-0.2.2/RcppCCTZ/src/time_zone_fixed.cc |only RcppCCTZ-0.2.2/RcppCCTZ/src/time_zone_format.cc | 230 ++--- RcppCCTZ-0.2.2/RcppCCTZ/src/time_zone_impl.cc | 21 RcppCCTZ-0.2.2/RcppCCTZ/src/time_zone_info.cc | 688 ++++++++------- RcppCCTZ-0.2.2/RcppCCTZ/src/time_zone_libc.cc | 112 +- RcppCCTZ-0.2.2/RcppCCTZ/src/time_zone_lookup.cc | 82 + RcppCCTZ-0.2.2/RcppCCTZ/src/time_zone_posix.cc | 18 RcppCCTZ-0.2.2/RcppCCTZ/src/utilities.cpp | 12 26 files changed, 1001 insertions(+), 740 deletions(-)
Title: Functions to Support Extension Education Program Evaluation
Description: Functions and datasets to support "Summary and Analysis of
Extension Education Program Evaluation in R" and "An R
Companion for the Handbook of Biological Statistics".
Vignettes are available at <http://rcompanion.org>.
Author: Salvatore Mangiafico [aut, cre]
Maintainer: Salvatore Mangiafico <mangiafico@njaes.rutgers.edu>
Diff between rcompanion versions 1.5.0 dated 2017-03-03 and 1.5.6 dated 2017-04-21
DESCRIPTION | 10 +- MD5 | 116 +++++++++++++++---------------- R/groupwiseMedian.r | 8 +- R/nagelkerke.r | 87 ++++++++++++++++++----- R/nagelkerkeHermite.r | 30 ++++++-- man/Anderson.Rd | 1 man/AndersonBias.Rd | 1 man/AndersonRainBarrel.Rd | 1 man/AndersonRainGarden.Rd | 1 man/BobBelcher.Rd | 1 man/Breakfast.Rd | 1 man/BrendonSmall.Rd | 1 man/BullyHill.Rd | 1 man/Catbus.Rd | 1 man/HayleySmith.Rd | 1 man/Monarchs.Rd | 1 man/Nurseries.Rd | 1 man/Pooh.Rd | 1 man/PoohPiglet.Rd | 1 man/Religion.Rd | 1 man/cateNelson.Rd | 7 - man/cldList.Rd | 7 - man/compareGLM.Rd | 7 - man/compareLM.Rd | 7 - man/fullPTable.Rd | 7 - man/groupwiseCMH.Rd | 7 - man/groupwiseGeometric.Rd | 7 - man/groupwiseHuber.Rd | 7 - man/groupwiseMean.Rd | 7 - man/groupwiseMedian.Rd | 15 ++-- man/groupwiseSum.Rd | 7 - man/nagelkerke.Rd | 54 ++++++++++---- man/nagelkerkeHermite.Rd | 20 +++-- man/nominalSymmetryTest.Rd | 7 - man/pairwiseDifferences.Rd | 7 - man/pairwiseMcnemar.Rd | 7 - man/pairwiseMedianMatrix.Rd | 7 - man/pairwiseMedianTest.Rd | 7 - man/pairwiseModelAnova.Rd | 7 - man/pairwiseNominalIndependence.Rd | 7 - man/pairwiseNominalMatrix.Rd | 7 - man/pairwiseOrdinalIndependence.Rd | 7 - man/pairwiseOrdinalMatrix.Rd | 7 - man/pairwiseOrdinalPairedMatrix.Rd | 7 - man/pairwiseOrdinalPairedTest.Rd | 7 - man/pairwiseOrdinalTest.Rd | 7 - man/pairwisePermutationMatrix.Rd | 7 - man/pairwisePermutationSymmetry.Rd | 7 - man/pairwisePermutationSymmetryMatrix.Rd | 7 - man/pairwisePermutationTest.Rd | 7 - man/pairwiseRobustMatrix.Rd | 7 - man/pairwiseRobustTest.Rd | 7 - man/pairwiseSignMatrix.Rd | 7 - man/pairwiseSignTest.Rd | 7 - man/plotDensityHistogram.Rd | 7 - man/plotNormalDensity.Rd | 7 - man/plotNormalHistogram.Rd | 7 - man/plotPredy.Rd | 7 - man/transformTukey.Rd | 7 - 59 files changed, 331 insertions(+), 276 deletions(-)
Title: Calculations and Visualisations Related to Geometric
Morphometrics
Description: A toolset for Geometric Morphometrics and mesh processing. This
includes (among other stuff) mesh deformations based on reference points,
permutation tests, detection of outliers, processing of sliding
semi-landmarks and semi-automated surface landmark placement.
Author: Stefan Schlager [aut, cre, cph],
Gregory Jefferis [ctb]
Maintainer: Stefan Schlager <zarquon42@gmail.com>
Diff between Morpho versions 2.5 dated 2017-04-05 and 2.5.1 dated 2017-04-21
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/Morpho-package.R | 4 ++-- R/procSym.r | 4 +++- inst/NEWS.Rd | 10 ++++++++++ man/Morpho-package.Rd | 4 ++-- 6 files changed, 26 insertions(+), 14 deletions(-)
Title: Memoisation of Functions
Description: Cache the results of a function so that when you call it
again with the same arguments it returns the pre-computed value.
Author: Hadley Wickham [aut],
Jim Hester [aut, cre],
Kirill Müller [aut],
Daniel Cook [aut]
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between memoise versions 1.0.0 dated 2016-01-29 and 1.1.0 dated 2017-04-21
memoise-1.0.0/memoise/R/cache.r |only memoise-1.0.0/memoise/R/memoise.r |only memoise-1.1.0/memoise/DESCRIPTION | 17 ++- memoise-1.1.0/memoise/LICENSE | 2 memoise-1.1.0/memoise/MD5 | 34 ++++--- memoise-1.1.0/memoise/NAMESPACE | 3 memoise-1.1.0/memoise/NEWS.md | 10 +- memoise-1.1.0/memoise/R/cache_filesystem.R |only memoise-1.1.0/memoise/R/cache_memory.R |only memoise-1.1.0/memoise/R/cache_s3.R |only memoise-1.1.0/memoise/R/memoise.R |only memoise-1.1.0/memoise/README.md | 77 +++++++++++++++-- memoise-1.1.0/memoise/man/cache_filesystem.Rd |only memoise-1.1.0/memoise/man/cache_memory.Rd |only memoise-1.1.0/memoise/man/cache_s3.Rd |only memoise-1.1.0/memoise/man/forget.Rd | 3 memoise-1.1.0/memoise/man/has_cache.Rd | 3 memoise-1.1.0/memoise/man/is.memoised.Rd | 3 memoise-1.1.0/memoise/man/memoise.Rd | 11 +- memoise-1.1.0/memoise/man/timeout.Rd | 3 memoise-1.1.0/memoise/tests/testthat/helper.R |only memoise-1.1.0/memoise/tests/testthat/test-filesystem.R |only memoise-1.1.0/memoise/tests/testthat/test-memoise.R | 54 +++++++++-- memoise-1.1.0/memoise/tests/testthat/test-s3.R |only 24 files changed, 167 insertions(+), 53 deletions(-)
Title: Hotelling's T^2 Test and Variants
Description: A set of R functions which implements Hotelling's T^2 test and some variants of it. Functions are also included for Aitchison's additive log ratio and centred log ratio transformations.
Author: James Curran [aut, cre]
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between Hotelling versions 1.0-2 dated 2013-11-06 and 1.0-3 dated 2017-04-21
DESCRIPTION | 19 - MD5 | 33 +- NAMESPACE | 27 +- R/Hotelling-package.R |only R/alr.R | 77 ++++-- R/clr.R | 86 +++++-- R/hotelling.test.r | 519 +++++++++++++++++++++++++++++--------------- README.md |only data/bottle.df.txt.gz |binary data/container.df.txt.gz |binary man/Hotelling-package.Rd |only man/alr.Rd | 96 ++++---- man/bottle.df.Rd | 33 +- man/clr.Rd | 91 ++++--- man/container.df.Rd | 36 +-- man/hotelling.stat.Rd | 117 +++++---- man/hotelling.test.Rd | 195 +++++++++------- man/plot.hotelling.test.Rd | 68 +++-- man/print.hotelling.test.Rd | 66 +++-- 19 files changed, 888 insertions(+), 575 deletions(-)
Title: Generalized Additive Models
Description: Functions for fitting and working with generalized
additive models, as described in chapter 7 of "Statistical Models in
S" (Chambers and Hastie (eds), 1991), and "Generalized Additive
Models" (Hastie and Tibshirani, 1990).
Author: Trevor Hastie
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between gam versions 1.14 dated 2016-09-10 and 1.14-3 dated 2017-04-21
gam-1.14-3/gam/ChangeLog | 4 + gam-1.14-3/gam/DESCRIPTION | 8 +-- gam-1.14-3/gam/INDEX | 1 gam-1.14-3/gam/MD5 | 28 ++++++------ gam-1.14-3/gam/NAMESPACE | 6 +- gam-1.14-3/gam/R/gam.R | 1 gam-1.14-3/gam/R/gam.fit.R | 67 ++++++++++++++-------------- gam-1.14-3/gam/R/gam.random.R | 36 ++++++++------- gam-1.14-3/gam/R/gam.smoothers.R |only gam-1.14-3/gam/R/na.gam.replace.R | 84 +++++++++++++++++------------------- gam-1.14-3/gam/R/random.R | 20 ++++---- gam-1.14-3/gam/man/gam-internal.Rd | 4 - gam-1.14-3/gam/man/gam.smoothers.Rd |only gam-1.14-3/gam/man/random.Rd |only gam-1.14-3/gam/man/s.Rd | 23 ++++++--- gam-1.14-3/gam/src/gam_init.c |only gam-1.14/gam/R/gam.slist.R |only gam-1.14/gam/R/gam.wlist.R |only 18 files changed, 147 insertions(+), 135 deletions(-)
Title: Family REGional Association Tests
Description: Fast regional association analysis of quantitative traits for family-based and population studies.
Author: Nadezhda M. Belonogova <belon@bionet.nsc.ru> and
Gulnara R. Svishcheva <gulsvi@mail.ru>,
with contributions from:
Seunggeun Lee (kernel functions), Pierre Lafaye de Micheaux ('davies' method),
Thomas Lumley ('kuonen' method), James O. Ramsay (functional data analysis functions),
David Clayton ('read.plink' function) and Brian Ripley ('ginv' function)
Maintainer: Nadezhda M. Belonogova <belon@bionet.nsc.ru>
Diff between FREGAT versions 1.0.2 dated 2016-09-19 and 1.0.3 dated 2017-04-21
CHANGES |only DESCRIPTION | 6 ++-- MD5 | 40 +++++++++++++++------------- NAMESPACE | 6 ++-- R/check.input.R | 1 R/check.spec.R | 18 +++--------- R/do.regional.R | 35 ++++++++++++++++++++++--- R/fixed.effects.R | 2 + R/genotypes.R | 63 +++++++++++++++++++++++++++++---------------- R/main.R | 12 ++++---- R/null.R | 1 R/polylik.R | 37 ++++++++++++++++++++------ R/random.effects.R | 2 - inst/doc/FREGAT-manual.pdf |binary man/FFBSKAT.rd | 7 +++-- man/MLR.rd | 5 ++- man/famBT.rd | 8 ++++- man/famFLM.rd | 47 ++++++++++++++++++++++++++++++--- man/null.rd | 4 ++ man/read.plink.rd | 2 - src/FREGAT_init.c |only src/ruben.cpp | 1 22 files changed, 206 insertions(+), 91 deletions(-)
Title: Statistical Inference for Parametric and Semiparametric Models
Based on Dependently Truncated Data
Description: Suppose that one can observe bivariate random variables (X, Y) only when X<=Y holds. Data (Xj, Yj), subject to Xj<=Yj, for all j=1,...,n, are called truncated data. For truncated data, several different approaches are implemented for statistical inference on (X, Y), when X and Y are dependent. Also included is truncated data on the number of deaths at each year (1963-1980) for Japanese male centenarians.
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between depend.truncation versions 2.5 dated 2016-04-14 and 2.6 dated 2017-04-21
DESCRIPTION | 8 +++--- MD5 | 10 ++++--- R/PMLE.Clayton.Exponential.R |only man/PMLE.Clayton.Exponential.Rd |only man/PMLE.Clayton.Weibull.Rd | 50 ++++++++++++++++++++++----------------- man/depend.truncation-package.Rd | 12 ++++----- man/dependAFT.reg.Rd | 2 - 7 files changed, 46 insertions(+), 36 deletions(-)
More information about depend.truncation at CRAN
Permanent link
Title: Tools for Data Manipulation
Description: An implementation of common higher order functions with syntactic
sugar for anonymous function. Provides also a link to 'dplyr' for common
transformations on data frames to work around non standard evaluation by
default.
Author: Sebastian Warnholz [aut, cre]
Maintainer: Sebastian Warnholz <wahani@gmail.com>
Diff between dat versions 0.1.0 dated 2017-01-06 and 0.2.0 dated 2017-04-21
DESCRIPTION | 8 ++--- MD5 | 55 ++++++++++++++++++++-------------------- NEWS | 13 +++++++++ R/DataFrame.R | 6 +--- R/NAMESPACE.R | 13 ++++++++- R/bindRows.R | 16 ++++++----- R/extract.R | 5 +-- R/helper.R | 18 ++++++++++--- R/replace.R | 2 - build/vignette.rds |binary inst/doc/Introduction.R | 3 ++ inst/doc/Introduction.Rmd | 9 ++++++ inst/doc/Introduction.html | 19 +++++++------ inst/doc/performance.html | 2 - man/DataFrame.Rd | 6 ++-- man/FormulaList.Rd | 1 man/as.function.formula.Rd | 1 man/bindRows.Rd | 12 ++++---- man/extract.Rd | 11 +++----- man/map.Rd | 11 +++----- man/mutar.Rd | 3 -- man/reexports.Rd | 4 +- man/replace.Rd | 7 ++--- man/verboseApply.Rd | 1 tests/testthat/test-DataFrame.R | 18 ------------- tests/testthat/test-S4attach.R |only tests/testthat/test-map.R | 1 tests/testthat/test-mutar.R | 37 ++++++++++++++++++++++++++ vignettes/Introduction.Rmd | 9 ++++++ 29 files changed, 180 insertions(+), 111 deletions(-)
Title: Cross-Screening in Observational Studies that Test Many
Hypotheses
Description: Cross-screening is a new method that uses both random halves of the sample to screen and test many hypotheses. It generally improves statistical power in observational studies when many hypotheses are tested simultaneously. References: 1. Qingyuan Zhao, Dylan S Small, and Paul R Rosenbaum. Cross-screening in observational studies that test many hypotheses. <arXiv:1703.02078>. 2. Qingyuan Zhao. On sensitivity value of pair-matched observational studies. <arXiv:1702.03442>.
Author: Paul Rosenbaum [aut],
Qingyuan Zhao [aut, cre]
Maintainer: Qingyuan Zhao <qyzhao@wharton.upenn.edu>
Diff between CrossScreening versions 0.0.1 dated 2017-03-12 and 0.1.1 dated 2017-04-21
CrossScreening-0.0.1/CrossScreening/man/gamma.to.kappa.Rd |only CrossScreening-0.0.1/CrossScreening/man/get.kappa.Rd |only CrossScreening-0.0.1/CrossScreening/man/kappa.to.gamma.Rd |only CrossScreening-0.1.1/CrossScreening/DESCRIPTION | 16 CrossScreening-0.1.1/CrossScreening/MD5 | 35 - CrossScreening-0.1.1/CrossScreening/NAMESPACE | 9 CrossScreening-0.1.1/CrossScreening/R/core.R | 437 ++++++++++--- CrossScreening-0.1.1/CrossScreening/R/example.R | 76 ++ CrossScreening-0.1.1/CrossScreening/R/sim.R | 4 CrossScreening-0.1.1/CrossScreening/build |only CrossScreening-0.1.1/CrossScreening/data/lead.rda |only CrossScreening-0.1.1/CrossScreening/data/methotrexate.rda |only CrossScreening-0.1.1/CrossScreening/inst |only CrossScreening-0.1.1/CrossScreening/man/cross.screen.Rd | 34 - CrossScreening-0.1.1/CrossScreening/man/fallback.test.Rd | 2 CrossScreening-0.1.1/CrossScreening/man/kappa2gamma.Rd |only CrossScreening-0.1.1/CrossScreening/man/lead.Rd |only CrossScreening-0.1.1/CrossScreening/man/methotrexate.Rd |only CrossScreening-0.1.1/CrossScreening/man/multrnks.Rd |only CrossScreening-0.1.1/CrossScreening/man/nhanes.log2diff.Rd |only CrossScreening-0.1.1/CrossScreening/man/power.sen.Rd |only CrossScreening-0.1.1/CrossScreening/man/sen.Rd | 48 + CrossScreening-0.1.1/CrossScreening/man/sen.ci.Rd |only CrossScreening-0.1.1/CrossScreening/man/sen.value.Rd |only CrossScreening-0.1.1/CrossScreening/vignettes |only 25 files changed, 527 insertions(+), 134 deletions(-)
More information about CrossScreening at CRAN
Permanent link
Title: Easily Download and Visualise Climate Data from CliFlo
Description: CliFlo is a web portal to the New Zealand National Climate
Database and provides public access (via subscription) to around 6,500
various climate stations (see <https://cliflo.niwa.co.nz/> for more
information). Collating and manipulating data from CliFlo
(hence clifro) and importing into R for further analysis, exploration and
visualisation is now straightforward and coherent. The user is required to
have an internet connection, and a current CliFlo subscription (free) if
data from stations, other than the public Reefton electronic weather
station, is sought.
Author: Blake Seers [aut, cre]
Maintainer: Blake Seers <blake.seers@gmail.com>
Diff between clifro versions 3.1-3 dated 2017-03-16 and 3.1-4 dated 2017-04-21
DESCRIPTION | 10 +++++----- MD5 | 26 +++++++++++++++++--------- NEWS.md | 5 +++++ R/cfUser.R | 10 ++++++++-- README.md | 6 ++++-- build/vignette.rds |binary inst/doc/cfStation.html | 6 +++--- inst/doc/choose-datatype.html | 6 +++--- inst/doc/choose-station.html | 6 +++--- inst/doc/clifro.html | 6 +++--- tests |only 11 files changed, 51 insertions(+), 30 deletions(-)