Title: Aggregate Longitudinal Survey Data
Description: Aggregate Business Tendency Survey Data (and other qualitative
surveys) to time series at various aggregation levels. Run aggregation of
survey data in a speedy, re-traceable and a easily deployable way.
Aggregation is substantially accelerated by use of data.table.
This package intends to provide an interface that is less general and abstract than data.table but rather geared towards
survey researchers.
Author: Matthias Bannert [aut, cre],
Gabriel Bucur [aut]
Maintainer: Matthias Bannert <bannert@kof.ethz.ch>
Diff between panelaggregation versions 0.1 dated 2014-12-03 and 0.1.1 dated 2017-01-06
DESCRIPTION | 21 ++++++++++++++------- MD5 | 22 +++++++++++----------- NAMESPACE | 6 +++++- R/computeShares.R | 5 ++++- R/computeWeightedMeans.R | 1 + man/btsdemo.Rd | 7 ++++--- man/computeBalance.Rd | 3 ++- man/computeShares.Rd | 5 +++-- man/computeWeightedMeans.Rd | 5 +++-- man/doUniqueCJ.Rd | 3 ++- man/extractTimeSeries.Rd | 3 ++- man/joinDataTables.Rd | 3 ++- 12 files changed, 53 insertions(+), 31 deletions(-)
More information about panelaggregation at CRAN
Permanent link
Title: R Bindings for ZeroMQ
Description: Interface to the 'ZeroMQ' lightweight messaging kernel (see <http://www.zeromq.org/> for more information).
Author: Whit Armstrong [aut, cre],
Jeroen Ooms [aut]
Maintainer: Whit Armstrong <armstrong.whit@gmail.com>
Diff between rzmq versions 0.7.7 dated 2014-12-09 and 0.9.0 dated 2017-01-06
rzmq-0.7.7/rzmq/inst/cppzmq |only rzmq-0.7.7/rzmq/src/Makevars |only rzmq-0.7.7/rzmq/src/cppzmq.h |only rzmq-0.9.0/rzmq/DESCRIPTION | 17 +++++++++++------ rzmq-0.9.0/rzmq/MD5 | 26 ++++++++++++++------------ rzmq-0.9.0/rzmq/NAMESPACE | 1 + rzmq-0.9.0/rzmq/R/rzmq.R | 9 +++++++-- rzmq-0.9.0/rzmq/README.md |only rzmq-0.9.0/rzmq/cleanup |only rzmq-0.9.0/rzmq/configure |only rzmq-0.9.0/rzmq/inst/zmq.hpp |only rzmq-0.9.0/rzmq/man/connect.socket.Rd | 2 ++ rzmq-0.9.0/rzmq/man/send.socket.Rd | 3 ++- rzmq-0.9.0/rzmq/src/Makevars.in |only rzmq-0.9.0/rzmq/src/Makevars.win |only rzmq-0.9.0/rzmq/src/interface.cpp | 31 +++++++++++++++++++++++++++++-- rzmq-0.9.0/rzmq/src/interface.h | 1 + rzmq-0.9.0/rzmq/tools |only 18 files changed, 67 insertions(+), 23 deletions(-)
Title: Generalized Dissimilarity Modeling
Description: A toolkit with functions to fit, plot, and summarize Generalized Dissimilarity Models (Ferrier et al. 2007, <doi:10.1111/j.1472-4642.2007.00341.x>).
Author: Glenn Manion, Matthew Lisk, Simon Ferrier, Diego Nieto-Lugilde, Karel Mokany, Matthew C. Fitzpatrick
Maintainer: Matthew C. Fitzpatrick <mfitzpatrick@umces.edu>
Diff between gdm versions 1.2.3 dated 2016-04-15 and 1.3.0 dated 2017-01-06
gdm-1.2.3/gdm/man/gd.varImp.Rd |only gdm-1.3.0/gdm/DESCRIPTION | 16 gdm-1.3.0/gdm/MD5 | 22 - gdm-1.3.0/gdm/R/GDM_Table_Funcs.R | 547 ++++++++++++++++++--------- gdm-1.3.0/gdm/build/vignette.rds |binary gdm-1.3.0/gdm/data/gdm.RData |binary gdm-1.3.0/gdm/man/formatsitepair.Rd | 34 - gdm-1.3.0/gdm/man/gdm.Rd | 8 gdm-1.3.0/gdm/man/gdm.varImp.Rd |only gdm-1.3.0/gdm/man/plot.gdm.Rd | 2 gdm-1.3.0/gdm/man/plotUncertainty.Rd | 18 gdm-1.3.0/gdm/man/predict.gdm.Rd | 4 gdm-1.3.0/gdm/man/removeSitesFromSitePair.Rd | 36 + 13 files changed, 443 insertions(+), 244 deletions(-)
Title: Elliptic Distribution and Lambda Option Pricing Model
Description: An implementation of the univariate elliptic distribution, and
lambda option pricing model. It provides detailed functionality and data
sets for the distribution and modelling. Especially, it contains functions
for the computation of density, probability, quantile, fitting procedures,
option prices, volatility smile. It also comes with sample financial data,
and plotting routines.
Author: Stephen H-T. Lihn [aut, cre]
Maintainer: Stephen H-T. Lihn <stevelihn@gmail.com>
Diff between ecd versions 0.8.2 dated 2016-07-10 and 0.8.3 dated 2017-01-06
ecd-0.8.2/ecd/R/ecld.quartic-RN0-method.R |only ecd-0.8.3/ecd/DESCRIPTION | 41 ++++--- ecd-0.8.3/ecd/MD5 | 57 ++++++---- ecd-0.8.3/ecd/NAMESPACE | 19 +++ ecd-0.8.3/ecd/NEWS.md | 5 ecd-0.8.3/ecd/R/ecd-diff-method.R |only ecd-0.8.3/ecd/R/ecd-read-csv-by-symbol-method.R | 4 ecd-0.8.3/ecd/R/ecld-constructor.R | 31 +++++ ecd-0.8.3/ecd/R/ecld-fixed-point-RN0-method.R |only ecd-0.8.3/ecd/R/ecld-mgf-term-method.R | 31 +++++ ecd-0.8.3/ecd/R/ecld-mpnum-method.R | 7 - ecd-0.8.3/ecd/R/ecld-mu-D-method.R | 1 ecd-0.8.3/ecd/R/ecld-ogf-method.R | 27 ++-- ecd-0.8.3/ecd/R/ecld-op-Q-method.R |only ecd-0.8.3/ecd/R/ecld-op-V-method.R | 17 +- ecd-0.8.3/ecd/R/ecld-quartic-RN0-method.R |only ecd-0.8.3/ecd/R/ecop-find-fixed-point-lambda-by-atm-skew-method.R |only ecd-0.8.3/ecd/R/ecop-find-fixed-point-sd-by-lambda-method.R |only ecd-0.8.3/ecd/R/ecop-get-ld-triple-method.R |only ecd-0.8.3/ecd/R/ecop-term-plot-3x3-method.R | 6 + ecd-0.8.3/ecd/R/ecop-vix-plot-3x3-method.R |only ecd-0.8.3/ecd/inst/extdata/data_conf.yml | 7 + ecd-0.8.3/ecd/inst/extdata/spx_archive_7.csv.zip |binary ecd-0.8.3/ecd/inst/extdata/vix_archive_7.csv.zip |binary ecd-0.8.3/ecd/inst/extdata/vxv_archive_7.csv.zip |only ecd-0.8.3/ecd/man/ecd.diff.Rd |only ecd-0.8.3/ecd/man/ecld.Rd | 9 + ecd-0.8.3/ecd/man/ecld.fixed_point_SN0_atm_ki.Rd |only ecd-0.8.3/ecd/man/ecld.mgf_term.Rd | 6 - ecd-0.8.3/ecd/man/ecld.op_Q.Rd |only ecd-0.8.3/ecd/man/ecld.op_V.Rd | 6 - ecd-0.8.3/ecd/man/ecld.quartic_SN0_atm_ki.Rd | 2 ecd-0.8.3/ecd/man/ecop.find_fixed_point_lambda_by_atm_skew.Rd |only ecd-0.8.3/ecd/man/ecop.find_fixed_point_sd_by_lambda.Rd |only ecd-0.8.3/ecd/man/ecop.get_ld_triple.Rd |only ecd-0.8.3/ecd/man/ecop.vix_plot_3x3.Rd |only ecd-0.8.3/ecd/tests/testthat/test-lambda-gamma-ecd.R | 8 + ecd-0.8.3/ecd/tests/testthat/test-option-ecop.R | 56 +++++++++ 38 files changed, 271 insertions(+), 69 deletions(-)
Title: Identify Similar Cases for Qualitative Case Studies
Description: Allows users to identify similar cases for qualitative case studies using statistical matching methods.
Author: Rich Nielsen
Maintainer: Rich Nielsen <rnielsen@mit.edu>
Diff between caseMatch versions 1.0.6 dated 2016-03-01 and 1.0.7 dated 2017-01-06
DESCRIPTION | 8 +- MD5 | 8 +- R/case.match.R | 128 +++++++++++++++++++++++++++++++++++++++++++++++ man/case.match.Rd | 7 +- man/caseMatch-package.Rd | 6 +- 5 files changed, 143 insertions(+), 14 deletions(-)
Title: Applied Econometrics with R
Description: Functions, data sets, examples, demos, and vignettes for the book
Christian Kleiber and Achim Zeileis (2008),
Applied Econometrics with R, Springer-Verlag, New York.
ISBN 978-0-387-77316-2. (See the vignette "AER" for a package overview.)
Author: Christian Kleiber [aut],
Achim Zeileis [aut, cre]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between AER versions 1.2-4 dated 2015-06-06 and 1.2-5 dated 2017-01-06
DESCRIPTION | 21 +- MD5 | 342 +++++++++++++++++------------------ NEWS | 14 + R/ivreg.R | 27 +- R/tobit.R | 3 build/vignette.rds |binary data/Affairs.rda |binary data/ArgentinaCPI.rda |binary data/BankWages.rda |binary data/BenderlyZwick.rda |binary data/BondYield.rda |binary data/CASchools.rda |binary data/CPS1985.rda |binary data/CPS1988.rda |binary data/CPSSW04.rda |binary data/CPSSW3.rda |binary data/CPSSW8.rda |binary data/CPSSW9204.rda |binary data/CPSSW9298.rda |binary data/CPSSWEducation.rda |binary data/CartelStability.rda |binary data/ChinaIncome.rda |binary data/CigarettesB.rda |binary data/CigarettesSW.rda |binary data/CollegeDistance.rda |binary data/ConsumerGood.rda |binary data/CreditCard.rda |binary data/DJFranses.rda |binary data/DJIA8012.rda |only data/DoctorVisits.rda |binary data/DutchAdvert.rda |binary data/DutchSales.rda |binary data/Electricity1955.rda |binary data/Electricity1970.rda |binary data/EquationCitations.rda |binary data/Equipment.rda |binary data/EuroEnergy.rda |binary data/Fatalities.rda |binary data/Fertility.rda |binary data/Fertility2.rda |binary data/FrozenJuice.rda |binary data/GSOEP9402.rda |binary data/GSS7402.rda |binary data/GermanUnemployment.rda |binary data/GoldSilver.rda |only data/GrowthDJ.rda |binary data/GrowthSW.rda |binary data/Grunfeld.rda |binary data/Guns.rda |binary data/HMDA.rda |binary data/HealthInsurance.rda |binary data/HousePrices.rda |binary data/Journals.rda |binary data/KleinI.rda |binary data/Longley.rda |binary data/MASchools.rda |binary data/MSCISwitzerland.rda |only data/ManufactCosts.rda |binary data/MarkDollar.rda |binary data/MarkPound.rda |binary data/Medicaid1986.rda |binary data/Mortgage.rda |binary data/MotorCycles.rda |binary data/MotorCycles2.rda |only data/Municipalities.rda |binary data/MurderRates.rda |binary data/NMES1988.rda |binary data/NYSESW.rda |binary data/NaturalGas.rda |binary data/OECDGas.rda |binary data/OECDGrowth.rda |binary data/OlympicTV.rda |binary data/OrangeCounty.rda |binary data/PSID1976.rda |binary data/PSID1982.rda |binary data/PSID7682.rda |binary data/Parade2005.rda |binary data/PepperPrice.rda |binary data/PhDPublications.rda |binary data/ProgramEffectiveness.rda |binary data/RecreationDemand.rda |binary data/ResumeNames.rda |binary data/SIC33.rda |binary data/STAR.rda |binary data/ShipAccidents.rda |binary data/SmokeBan.rda |binary data/SportsCards.rda |binary data/StrikeDuration.rda |binary data/SwissLabor.rda |binary data/TeachingRatings.rda |binary data/TechChange.rda |binary data/TradeCredit.rda |binary data/TravelMode.rda |binary data/UKInflation.rda |binary data/UKNonDurables.rda |binary data/USAirlines.rda |binary data/USConsump1950.rda |binary data/USConsump1979.rda |binary data/USConsump1993.rda |binary data/USCrudes.rda |binary data/USGasB.rda |binary data/USGasG.rda |binary data/USInvest.rda |binary data/USMacroB.rda |binary data/USMacroG.rda |binary data/USMacroSW.rda |binary data/USMacroSWM.rda |binary data/USMacroSWQ.rda |binary data/USMoney.rda |binary data/USProdIndex.rda |binary data/USSeatBelts.rda |binary data/USStocksSW.rda |binary data/WeakInstrument.rda |binary data/datalist | 4 inst/CITATION | 4 inst/doc/AER.R | 8 inst/doc/AER.Rnw | 45 +++- inst/doc/AER.pdf |binary inst/doc/Sweave-journals.pdf |binary man/ArgentinaCPI.Rd | 13 + man/CASchools.Rd | 2 man/CPS1988.Rd | 2 man/CPSSW.Rd | 2 man/CartelStability.Rd | 2 man/ChinaIncome.Rd | 2 man/CigarettesSW.Rd | 2 man/CollegeDistance.Rd | 2 man/ConsumerGood.Rd | 2 man/DJFranses.Rd | 2 man/DJIA8012.Rd |only man/DutchAdvert.Rd | 11 - man/DutchSales.Rd | 2 man/Fatalities.Rd | 2 man/Fertility.Rd | 2 man/Franses1998.Rd | 1 man/FrozenJuice.Rd | 2 man/GSOEP9402.Rd | 2 man/GSS7402.Rd | 2 man/GermanUnemployment.Rd | 2 man/GoldSilver.Rd |only man/GrowthSW.Rd | 2 man/Guns.Rd | 2 man/HMDA.Rd | 2 man/HealthInsurance.Rd | 2 man/Journals.Rd | 4 man/MASchools.Rd | 2 man/MSCISwitzerland.Rd |only man/MotorCycles.Rd | 6 man/MotorCycles2.Rd |only man/NMES1988.Rd | 11 - man/NYSESW.Rd | 2 man/OlympicTV.Rd | 2 man/PepperPrice.Rd | 7 man/ResumeNames.Rd | 2 man/STAR.Rd | 2 man/SmokeBan.Rd | 2 man/SportsCards.Rd | 2 man/StockWatson2007.Rd | 1 man/TeachingRatings.Rd | 2 man/UKNonDurables.Rd | 2 man/USMacroSW.Rd | 2 man/USMacroSWM.Rd | 2 man/USMacroSWQ.Rd | 2 man/USProdIndex.Rd | 2 man/USSeatBelts.Rd | 2 man/USStocksSW.Rd | 2 man/WeakInstrument.Rd | 2 tests/Ch-Basics.Rout.save | 8 tests/Ch-Intro.Rout.save | 6 tests/Ch-LinearRegression.Rout.save | 19 - tests/Ch-Microeconometrics.Rout.save | 8 tests/Ch-Programming.Rout.save | 6 tests/Ch-TimeSeries.Rout.save | 6 tests/Ch-Validation.Rout.save | 30 +-- vignettes/AER.Rnw | 45 +++- vignettes/aer.bib | 22 +- 176 files changed, 388 insertions(+), 356 deletions(-)
Title: Explorer of World Population Prospects
Description: Explore data in the 'wpp2015' (or 2012, 2010) package using a 'shiny' interface.
Author: Hana Sevcikova <hanas@uw.edu>
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between wppExplorer versions 2.0-1 dated 2016-12-02 and 2.0-2 dated 2017-01-06
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/wpp.R | 2 +- inst/explore/README.html | 2 +- man/wppExplorer-package.Rd | 4 ++-- 6 files changed, 17 insertions(+), 13 deletions(-)
Title: R Interface to a 'PostGIS' Database
Description: Provides an interface between R and
'PostGIS'-enabled 'PostgreSQL' databases to transparently transfer
spatial data. Both vector (points, lines, polygons) and raster
data are supported in read and write modes. Also provides
convenience functions to execute common procedures in
'PostgreSQL/PostGIS'.
Author: Mathieu Basille [aut],
David Bucklin [aut, cre]
Maintainer: David Bucklin <dbucklin@ufl.edu>
Diff between rpostgis versions 1.0.3 dated 2016-10-28 and 1.1.0 dated 2017-01-06
rpostgis-1.0.3/rpostgis/R/dbAddKey.R |only rpostgis-1.0.3/rpostgis/R/dbAsDate.R |only rpostgis-1.0.3/rpostgis/R/dbColumn.R |only rpostgis-1.0.3/rpostgis/R/dbComment.R |only rpostgis-1.0.3/rpostgis/R/dbDrop.R |only rpostgis-1.0.3/rpostgis/R/dbIndex.R |only rpostgis-1.0.3/rpostgis/R/dbSchema.R |only rpostgis-1.0.3/rpostgis/R/dbTableInfo.R |only rpostgis-1.0.3/rpostgis/R/dbUtils.R |only rpostgis-1.0.3/rpostgis/R/dbVacuum.R |only rpostgis-1.1.0/rpostgis/DESCRIPTION | 18 +- rpostgis-1.1.0/rpostgis/MD5 | 86 +++++---- rpostgis-1.1.0/rpostgis/NAMESPACE | 10 + rpostgis-1.1.0/rpostgis/NEWS | 198 +++++++++++++++++------ rpostgis-1.1.0/rpostgis/R/all_db_wrapper_fns.R |only rpostgis-1.1.0/rpostgis/R/data.R |only rpostgis-1.1.0/rpostgis/R/dbUtils_notExported.R |only rpostgis-1.1.0/rpostgis/R/dbWriteDataFrame.R |only rpostgis-1.1.0/rpostgis/R/pgGetBoundary.R | 12 - rpostgis-1.1.0/rpostgis/R/pgGetGeom.R | 124 +++++++++----- rpostgis-1.1.0/rpostgis/R/pgGetRast.R | 46 +++-- rpostgis-1.1.0/rpostgis/R/pgInsert.R | 86 ++++++--- rpostgis-1.1.0/rpostgis/R/pgInsertize.R | 52 +++++- rpostgis-1.1.0/rpostgis/R/pgMakePts.R | 3 rpostgis-1.1.0/rpostgis/R/pgWriteRast.R |only rpostgis-1.1.0/rpostgis/R/rpostgis-package.R | 13 - rpostgis-1.1.0/rpostgis/README.md | 11 - rpostgis-1.1.0/rpostgis/data |only rpostgis-1.1.0/rpostgis/man/dbAddKey.Rd | 8 rpostgis-1.1.0/rpostgis/man/dbAsDate.Rd | 2 rpostgis-1.1.0/rpostgis/man/dbBuildTableQuery.Rd | 2 rpostgis-1.1.0/rpostgis/man/dbColumn.Rd | 6 rpostgis-1.1.0/rpostgis/man/dbComment.Rd | 10 - rpostgis-1.1.0/rpostgis/man/dbConnCheck.Rd | 2 rpostgis-1.1.0/rpostgis/man/dbDrop.Rd | 10 - rpostgis-1.1.0/rpostgis/man/dbExistsTable.Rd | 2 rpostgis-1.1.0/rpostgis/man/dbIndex.Rd | 4 rpostgis-1.1.0/rpostgis/man/dbSchema.Rd | 2 rpostgis-1.1.0/rpostgis/man/dbTableInfo.Rd | 4 rpostgis-1.1.0/rpostgis/man/dbTableNameFix.Rd | 2 rpostgis-1.1.0/rpostgis/man/dbVacuum.Rd | 4 rpostgis-1.1.0/rpostgis/man/dbVersion.Rd | 2 rpostgis-1.1.0/rpostgis/man/dbWriteDataFrame.Rd |only rpostgis-1.1.0/rpostgis/man/pgGetBoundary.Rd | 12 - rpostgis-1.1.0/rpostgis/man/pgGetGeom.Rd | 14 - rpostgis-1.1.0/rpostgis/man/pgGetRast.Rd | 19 +- rpostgis-1.1.0/rpostgis/man/pgInsert.Rd | 47 +++-- rpostgis-1.1.0/rpostgis/man/pgInsertizeGeom.Rd | 16 + rpostgis-1.1.0/rpostgis/man/pgMakePts.Rd | 3 rpostgis-1.1.0/rpostgis/man/pgWriteRast.Rd |only rpostgis-1.1.0/rpostgis/man/roe_gps_data.Rd |only rpostgis-1.1.0/rpostgis/man/rpostgis.Rd | 12 - 52 files changed, 559 insertions(+), 283 deletions(-)
Title: Regularization Paths for SCAD and MCP Penalized Regression
Models
Description: Efficient algorithms for fitting regularization paths for linear or
logistic regression models penalized by MCP or SCAD, with optional additional
L2 penalty.
Author: Patrick Breheny [aut,cre]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between ncvreg versions 3.7-1 dated 2016-12-23 and 3.8-0 dated 2017-01-06
DESCRIPTION | 10 +++++----- MD5 | 29 +++++++++++++++-------------- NEWS | 5 +++++ R/ncvreg.R | 4 ++-- R/ncvsurv.R | 6 +++--- R/plot.ncvreg.R | 13 +++++++------ R/std.R | 1 + inst/doc/quick-start.pdf |binary inst/tests/ncvreg.R | 2 +- inst/tests/single-lambda.R |only man/ncvreg.Rd | 5 +++-- man/ncvsurv.Rd | 5 +++-- src/binomial.c | 12 +++++++----- src/cox-dh.c | 10 ++++++---- src/gaussian.c | 10 ++++++---- src/poisson.c | 12 +++++++----- 16 files changed, 71 insertions(+), 53 deletions(-)
Title: List with Defaults
Description: Provides a function that, as an alternative to base::list, allows
default values to be inherited from another list.
Author: Russell S. Pierce
Maintainer: Russell S. Pierce <russell.s.pierce@gmail.com>
Diff between listWithDefaults versions 1.0.0 dated 2015-11-13 and 1.1.0 dated 2017-01-06
listWithDefaults-1.0.0/listWithDefaults/ChangeLog |only listWithDefaults-1.1.0/listWithDefaults/DESCRIPTION | 16 +- listWithDefaults-1.1.0/listWithDefaults/MD5 | 17 +- listWithDefaults-1.1.0/listWithDefaults/NAMESPACE | 8 - listWithDefaults-1.1.0/listWithDefaults/NEWS.md |only listWithDefaults-1.1.0/listWithDefaults/R/listWithDefaults.R | 57 ++++------ listWithDefaults-1.1.0/listWithDefaults/README.md |only listWithDefaults-1.1.0/listWithDefaults/inst/NEWS.Rd | 18 +-- listWithDefaults-1.1.0/listWithDefaults/man/listWithDefaults.Rd | 54 ++++----- listWithDefaults-1.1.0/listWithDefaults/tests/testthat.R | 8 - listWithDefaults-1.1.0/listWithDefaults/tests/testthat/test.listWithDefault.R | 10 - 11 files changed, 96 insertions(+), 92 deletions(-)
More information about listWithDefaults at CRAN
Permanent link
Title: Probabilistic Verbal Autopsy Coding with 'InSilicoVA' Algorithm
Description: Computes individual causes of death and population cause-specific mortality fractions using the 'InSilicoVA' algorithm from McCormick et al (2016) <DOI:10.1080/01621459.2016.1152191>. It uses data derived from verbal autopsy (VA) interviews, in a format similar to the input of the widely used 'InterVA4' method. This package provides general model fitting and customization for 'InSilicoVA' algorithm and basic graphical visualization of the output.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@uw.edu>
Diff between InSilicoVA versions 1.1.2 dated 2016-03-29 and 1.1.3 dated 2017-01-06
DESCRIPTION | 10 +++++----- MD5 | 15 +++++++++------ R/get_indiv.r | 10 +++++----- R/insilico_core.r | 10 ++++++---- R/zzz.R | 4 ++-- data/probbase3.rda |only inst/NEWS.rd |only man/RandomVA1.Rd | 4 ++-- man/get.indiv.Rd | 6 +++--- man/probbase3.Rd |only 10 files changed, 32 insertions(+), 27 deletions(-)
Title: Misspecified Models for Gene-Environment Interaction
Description: First major functionality is to compute the bias in misspecified linear gene-environment interaction models. The most
generalized function for this objective is GE_bias(). However GE_bias() requires specification of many
higher order moments of covariates in the model. If users are unsure about how to calculate/estimate
these higher order moments, it may be easier to use GE_bias_normal_squaredmis(). This function places
many more assumptions on the covariates (most notably that they are all jointly generated from a multivariate
normal distribution) and is thus able to automatically calculate many of the higher order moments automatically,
necessitating only that the user specify some covariances. There are also functions to solve for the bias
through simulation and non-linear equation solvers, these can be used to check your work. Second major functionality
is to implement the Bootstrap Inference with Correct Sandwich (BICS) testing procedure, which we have found to provide better finite-sample
performance than other inference procedures for testing GxE interaction. More details on these functions
are available in Sun, Carroll, Christiani, and Lin, "Testing for Gene-Environment Interaction Under Exposure Misspecification"
(Submitted).
Author: Ryan Sun [aut, cre]
Maintainer: Ryan Sun <ryansun.work@gmail.com>
Diff between GEint versions 0.1.1 dated 2016-09-30 and 0.1.2 dated 2017-01-06
DESCRIPTION | 16 +- MD5 | 24 ++-- R/GE_bias.R | 45 +++++--- R/GE_bias_normal_squaredmis.R | 163 ++++++++++++++++++++--------- R/GE_nleqslv.R | 151 ++++++++++++++++++++++----- R/GE_scoreeq_sim.R | 92 ++++++++++++---- R/GE_test_moment_calcs.R | 216 ++++++++++++++++++++++++--------------- R/GE_translate_inputs.R | 105 ++++++++++++------ inst/doc/GEint_example.html | 12 +- man/GE_bias.Rd | 7 - man/GE_bias_normal_squaredmis.Rd | 14 +- man/GE_nleqslv.Rd | 7 - man/GE_test_moment_calcs.Rd | 6 - 13 files changed, 590 insertions(+), 268 deletions(-)
Title: R Interface to the Europe PubMed Central RESTful Web Service
Description: An R Client for the Europe PubMed Central RESTful Web Service. It
gives access to both metadata on life science literature and open access
full texts. Europe PMC indexes all PubMed content and other literature
sources including Agricola, a bibliographic database of citations to the
agricultural literature, or Biological Patents. In addition to bibliographic
metadata, the client allows users to fetch citations and reference lists.
Links between life-science literature and other EBI databases, including
ENA, PDB or ChEMBL are also accessible. No registration or API key is
required. See the vignettes for usage examples.
Author: Najko Jahn [aut, cre, cph]
Maintainer: Najko Jahn <najko.jahn@gmail.com>
Diff between europepmc versions 0.1.0 dated 2016-07-13 and 0.1.1 dated 2017-01-06
europepmc-0.1.0/europepmc/inst/doc/rebi-vignettes.R |only europepmc-0.1.0/europepmc/inst/doc/rebi-vignettes.Rmd |only europepmc-0.1.0/europepmc/inst/doc/rebi-vignettes.html |only europepmc-0.1.0/europepmc/vignettes/rebi-vignettes.Rmd |only europepmc-0.1.1/europepmc/DESCRIPTION | 8 europepmc-0.1.1/europepmc/MD5 | 74 europepmc-0.1.1/europepmc/NAMESPACE | 15 europepmc-0.1.1/europepmc/NEWS.md | 18 europepmc-0.1.1/europepmc/R/epmc_citations.r | 88 europepmc-0.1.1/europepmc/R/epmc_db.r | 79 europepmc-0.1.1/europepmc/R/epmc_db_count.r | 3 europepmc-0.1.1/europepmc/R/epmc_details.r | 96 - europepmc-0.1.1/europepmc/R/epmc_ftxt_book.r | 1 europepmc-0.1.1/europepmc/R/epmc_hits.r | 10 europepmc-0.1.1/europepmc/R/epmc_lablinks.r | 114 - europepmc-0.1.1/europepmc/R/epmc_lablinks_count.r | 21 europepmc-0.1.1/europepmc/R/epmc_refs.r | 97 - europepmc-0.1.1/europepmc/R/epmc_search.r | 214 +- europepmc-0.1.1/europepmc/R/epmc_tm.r | 128 - europepmc-0.1.1/europepmc/R/epmc_tm_count.r | 27 europepmc-0.1.1/europepmc/R/europepmc.r | 7 europepmc-0.1.1/europepmc/R/tmp.r |only europepmc-0.1.1/europepmc/R/utils.r | 160 + europepmc-0.1.1/europepmc/README.md | 957 +++++----- europepmc-0.1.1/europepmc/build/vignette.rds |binary europepmc-0.1.1/europepmc/inst/doc/introducing-europepmc.R |only europepmc-0.1.1/europepmc/inst/doc/introducing-europepmc.Rmd |only europepmc-0.1.1/europepmc/inst/doc/introducing-europepmc.html |only europepmc-0.1.1/europepmc/man/epmc_citations.Rd | 4 europepmc-0.1.1/europepmc/man/epmc_db.Rd | 6 europepmc-0.1.1/europepmc/man/epmc_details.Rd | 6 europepmc-0.1.1/europepmc/man/epmc_ftxt_book.Rd | 1 europepmc-0.1.1/europepmc/man/epmc_refs.Rd | 6 europepmc-0.1.1/europepmc/man/epmc_search.Rd | 29 europepmc-0.1.1/europepmc/man/epmc_search_.Rd |only europepmc-0.1.1/europepmc/man/epmc_tm.Rd | 4 europepmc-0.1.1/europepmc/tests/testthat/test_epmc_db.r | 2 europepmc-0.1.1/europepmc/tests/testthat/test_epmc_details.r | 29 europepmc-0.1.1/europepmc/tests/testthat/test_epmc_ftxt_book.r | 4 europepmc-0.1.1/europepmc/tests/testthat/test_epmc_hits.r | 3 europepmc-0.1.1/europepmc/tests/testthat/test_epmc_lablinks.r | 4 europepmc-0.1.1/europepmc/tests/testthat/test_epmc_search.r | 11 europepmc-0.1.1/europepmc/vignettes/introducing-europepmc.Rmd |only 43 files changed, 1409 insertions(+), 817 deletions(-)
Title: Simulating Community Assembly and Ecological Diversification
Using Ecospace Frameworks
Description: Implements stochastic simulations of community assembly (ecological
diversification) using customizable ecospace frameworks (functional trait
spaces). Provides a wrapper to calculate common ecological disparity and
functional ecology statistical dynamics as a function of species richness.
Functions are written so they will work in a parallel-computing environment.
Author: Phil Novack-Gottshall [aut, cre]
Maintainer: Phil Novack-Gottshall <pnovack-gottshall@ben.edu>
Diff between ecospace versions 1.0.0 dated 2015-10-29 and 1.1.1 dated 2017-01-06
DESCRIPTION | 19 ++++++++++--------- MD5 | 46 +++++++++++++++++++++++----------------------- NAMESPACE | 2 +- R/KWTraits.R | 14 +++++++------- R/calc_metrics.R | 19 +++++++++---------- R/create_ecospace.R | 15 +++++++-------- R/ecospace.R | 30 +++++++++++++++--------------- R/expansion.R | 13 ++++++------- R/neutral.R | 13 ++++++------- R/partitioning.R | 13 ++++++------- R/rbind_listdf.R | 4 ++-- R/redundancy.R | 13 ++++++------- man/KWTraits.Rd | 16 ++++++++-------- man/calc_metrics.Rd | 29 ++++++++++++++--------------- man/create_ecospace.Rd | 30 +++++++++++++++--------------- man/ecospace-package.Rd | 31 ++++++++++++++++--------------- man/expansion.Rd | 24 ++++++++++++------------ man/neutral.Rd | 20 ++++++++++---------- man/partitioning.Rd | 24 ++++++++++++------------ man/prep_data.Rd | 4 ++-- man/rbind_listdf.Rd | 9 +++++---- man/redundancy.Rd | 24 ++++++++++++------------ man/sample2.Rd | 2 +- man/unique2.Rd | 2 +- 24 files changed, 206 insertions(+), 210 deletions(-)
Title: Interface to Bold Systems 'API'
Description: A programmatic interface to the Web Service methods provided by
Bold Systems for genetic 'barcode' data. Functions include methods for
searching by sequences by taxonomic names, ids, collectors, and
institutions; as well as a function for searching for specimens, and
downloading trace files.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between bold versions 0.3.5 dated 2016-03-29 and 0.4.0 dated 2017-01-06
DESCRIPTION | 9 ++---- LICENSE | 2 - MD5 | 50 ++++++++++++++++++--------------- NAMESPACE | 7 ++++ NEWS.md | 41 ++++++++++++++++++++++----- R/bold-package.R | 2 - R/bold_filter.R |only R/bold_identify.R | 57 ++++++++++++++++++++------------------ R/bold_identify_parents.R |only R/bold_seq.R | 44 ++++++++++++++++++++--------- R/bold_seqspec.R | 37 +++++++++++++++--------- R/bold_specimens.R | 30 ++++++++++++-------- R/bold_tax_id.R | 21 ++++++++------ R/bold_tax_name.R | 15 ++++++---- R/bold_trace.R | 31 ++++++++++++-------- R/zzz.R | 21 ++++++++++---- README.md | 53 +++++++++++++++-------------------- build/vignette.rds |binary man/bold_filter.Rd |only man/bold_identify.Rd | 49 ++++++++++++++++++-------------- man/bold_identify_parents.Rd |only man/bold_seq.Rd | 15 ++++++---- man/bold_seqspec.Rd | 22 +++++++++----- man/bold_specimens.Rd | 7 ++-- man/bold_tax_id.Rd | 11 ++++--- man/bold_tax_name.Rd | 8 ++--- man/bold_trace.Rd | 15 ++++++---- tests/testthat/test-bold_tax_id.R | 8 +++++ 28 files changed, 336 insertions(+), 219 deletions(-)
Title: Visual Exploration of Protein Alignments Resulting from Multiple
Substitution Matrices
Description: Substitution matrices are important parameters in protein alignment algorithms. These matrices represent the likelihood that an amino acid will be substituted for another during mutation. This tool allows users to apply predefined and custom matrices and then explore the resulting alignments with interactive visualizations. 'SubVis' requires the availability of a web browser.
Author: Scott Barlowe <sabarlowe@email.wcu.edu>
Maintainer: Scott Barlowe <sabarlowe@email.wcu.edu>
Diff between SubVis versions 1.1.0 dated 2016-06-29 and 2.0.0 dated 2017-01-06
DESCRIPTION | 10 MD5 | 34 inst/SubVisApp/global.R |only inst/SubVisApp/js/SubVisDraw.js | 236 ++-- inst/SubVisApp/js/SubVisEvents.js | 49 inst/SubVisApp/js/SubVisGetDecide.js | 14 inst/SubVisApp/js/SubVisGlobals.js | 19 inst/SubVisApp/server.R | 338 +++++- inst/SubVisApp/ui.R | 230 +++- inst/doc/SubVis.Rmd | 465 ++++++--- inst/doc/SubVis.html | 494 ++++++---- inst/extdata/Example_FASTA_files/Human.fasta |only inst/extdata/Example_FASTA_files/Xenla.fasta |only inst/extdata/Example_FASTA_files/fNucl.fasta |only inst/extdata/Example_FASTA_files/pFalc.fasta |only inst/extdata/Example_FASTA_files/tempPatt.fasta |only inst/extdata/Example_FASTA_files/tempSubj.fasta |only inst/extdata/Example_custom_matrix/BLS.txt |only inst/extdata/Example_custom_matrix/disorder.txt |only inst/extdata/Example_custom_matrix/falcNuc.txt |only inst/extdata/Example_custom_matrix/masterFile_gpcrtm.txt |only inst/extdata/Example_custom_matrix/masterFile_scaled_adj_bls.txt |only inst/extdata/Example_custom_matrix/scaled_BLSM.txt |only inst/extdata/Example_custom_matrix/scaled_adj_BLSM.txt |only vignettes/SubVis.Rmd | 465 ++++++--- 25 files changed, 1690 insertions(+), 664 deletions(-)
Title: Subgroup Identification Based on Differential Effect Search
Description: Provides function to apply "Subgroup Identification based on Differential Effect Search" (SIDES) method proposed by Lipkovich et al. (2011) <doi:10.1002/sim.4289>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between SIDES versions 1.8 dated 2016-12-20 and 1.9 dated 2017-01-06
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/SIDES_MAIN.R | 6 ++++-- man/SIDES-package.Rd | 4 ++-- 4 files changed, 13 insertions(+), 11 deletions(-)
Title: 'Lex' and 'Yacc'
Description: R implementation of the common parsing tools 'lex' and 'yacc'.
Author: Marek Jagielski [aut, cre, cph], David M. Beazley [aut, cph]
Maintainer: Marek Jagielski <marek.jagielski@gmail.com>
Diff between rly versions 1.3.0 dated 2016-12-29 and 1.4.0 dated 2017-01-06
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- NEWS.md | 6 ++++++ R/lex.R | 3 +++ tests/testthat/test.lex_literal4.R |only 5 files changed, 17 insertions(+), 7 deletions(-)
Title: Interactive Networks with R
Description: Create interactive networked coincidences. It joins the data analysis power of R to study coincidences and the visualization libraries of JavaScript in one package.
Author: Modesto Escobar <modesto@usal.es>,
Carlos Prieto <cprietos@usal.es>,
David Barrios <metal@usal.es>,
Luis Martinez-Uribe <lmartinez@usal.es>.
Maintainer: Modesto Escobar <modesto@usal.es>
Diff between netCoin versions 0.2.1 dated 2016-12-21 and 0.2.2 dated 2017-01-06
netCoin-0.2.1/netCoin/man/network.addLayout.Rd |only netCoin-0.2.1/netCoin/man/network.addLinkAttr.Rd |only netCoin-0.2.1/netCoin/man/network.addLinkFilter.Rd |only netCoin-0.2.1/netCoin/man/network.addNodeAttr.Rd |only netCoin-0.2.1/netCoin/man/network.addNodeFilter.Rd |only netCoin-0.2.1/netCoin/man/network.all.Rd |only netCoin-0.2.1/netCoin/man/network.create.Rd |only netCoin-0.2.1/netCoin/man/network.nodeImage.Rd |only netCoin-0.2.1/netCoin/man/network.nodePie.Rd |only netCoin-0.2.1/netCoin/man/network.start.Rd |only netCoin-0.2.2/netCoin/DESCRIPTION | 8 - netCoin-0.2.2/netCoin/MD5 | 40 ++---- netCoin-0.2.2/netCoin/NAMESPACE | 11 - netCoin-0.2.2/netCoin/R/barplot.R | 100 ++++++++-------- netCoin-0.2.2/netCoin/R/dichotomize.R | 29 ++-- netCoin-0.2.2/netCoin/R/netcoin.R | 126 +++++++++++++-------- netCoin-0.2.2/netCoin/data/sociologists.RData |only netCoin-0.2.2/netCoin/man/as.nodes.Rd | 7 - netCoin-0.2.2/netCoin/man/barCoin.Rd | 13 +- netCoin-0.2.2/netCoin/man/cbarCoin.Rd | 13 +- netCoin-0.2.2/netCoin/man/coin.Rd | 13 ++ netCoin-0.2.2/netCoin/man/dice.Rd | 6 - netCoin-0.2.2/netCoin/man/dichotomize.Rd | 4 netCoin-0.2.2/netCoin/man/expectedList.Rd | 11 + netCoin-0.2.2/netCoin/man/multigraph.create.Rd | 64 ++++++---- netCoin-0.2.2/netCoin/man/sociologists.Rd |only netCoin-0.2.2/netCoin/man/timeCoin.Rd | 5 27 files changed, 271 insertions(+), 179 deletions(-)
Title: An R Gallery for China and Other Geojson Choropleth Map in
Leaflet
Description: An R gallery for China and other geojson choropleth map in leaflet. Contains the geojson data for provinces, cities in China.
Author: Dawei Lang
Maintainer: Dawei Lang <chiffonlang@icloud.com>
Diff between leafletCN versions 0.1 dated 2016-12-30 and 0.2 dated 2017-01-06
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/demoMap.R | 2 +- R/geojsonMap.R | 23 +++++++++++++---------- R/leafletGeo.R | 17 +++++++++-------- man/demomap.Rd | 2 +- man/geojsonMap.Rd | 14 ++++++++------ man/leafletGeo.Rd | 10 +++++----- 8 files changed, 47 insertions(+), 41 deletions(-)
Title: STR Decomposition
Description: Methods for decomposing seasonal data: STR (a Seasonal-Trend decomposition procedure based on Regression) and Robust STR. In some ways, STR is similar to Ridge Regression and Robust STR can be related to LASSO. They allow for multiple seasonal components, multiple linear covariates with constant, flexible and seasonal influence. Seasonal patterns (for both seasonal components and seasonal covariates) can be fractional and flexible over time; moreover they can be either strictly periodic or have a more complex topology. The methods provide confidence intervals for the estimated components. The methods can be used for forecasting.
Author: Alexander Dokumentov, Rob J Hyndman
Maintainer: Alexander Dokumentov <alexander.dokumentov@gmail.com>
Diff between stR versions 0.2 dated 2016-09-10 and 0.3 dated 2017-01-06
stR-0.2/stR/vignettes/stRpackage.pdf |only stR-0.2/stR/vignettes/stRvignette_cache |only stR-0.2/stR/vignettes/stRvignette_files |only stR-0.3/stR/Changelog | 14 stR-0.3/stR/DESCRIPTION | 13 stR-0.3/stR/MD5 | 248 -- stR-0.3/stR/NAMESPACE | 82 stR-0.3/stR/R/RSTR.R | 6 stR-0.3/stR/R/STR.R | 171 - stR-0.3/stR/R/calls.R | 46 stR-0.3/stR/R/cg.R |only stR-0.3/stR/R/components.R | 94 - stR-0.3/stR/R/documentation.R | 5 stR-0.3/stR/R/electricity.R | 64 stR-0.3/stR/R/grocery.R | 44 stR-0.3/stR/R/heuristicSTR.R |only stR-0.3/stR/R/lmSolver.R |only stR-0.3/stR/R/lsmr.R |only stR-0.3/stR/R/mstsWrapper.R | 190 +- stR-0.3/stR/R/plot.str.R | 4 stR-0.3/stR/R/plotBeta.R |only stR-0.3/stR/R/seasadj.R | 110 - stR-0.3/stR/build/vignette.rds |binary stR-0.3/stR/inst/doc/stRvignette.R | 555 ++++++ stR-0.3/stR/inst/doc/stRvignette.Rmd | 427 +++- stR-0.3/stR/inst/doc/stRvignette.html | 931 +++++----- stR-0.3/stR/man/AutoSTR.Rd | 194 +- stR-0.3/stR/man/RSTRmodel.Rd | 314 +-- stR-0.3/stR/man/STR.Rd | 468 ++--- stR-0.3/stR/man/STRmodel.Rd | 315 +-- stR-0.3/stR/man/calls.Rd | 56 stR-0.3/stR/man/components.Rd | 58 stR-0.3/stR/man/confidence.Rd | 30 stR-0.3/stR/man/control.Rd | 26 stR-0.3/stR/man/data.Rd | 26 stR-0.3/stR/man/electricity.Rd | 72 stR-0.3/stR/man/gapCV.Rd | 28 stR-0.3/stR/man/grocery.Rd | 46 stR-0.3/stR/man/heuristicSTR.Rd |only stR-0.3/stR/man/lambdas.Rd | 32 stR-0.3/stR/man/nFold.Rd | 26 stR-0.3/stR/man/nMCIter.Rd | 26 stR-0.3/stR/man/pattern.Rd | 30 stR-0.3/stR/man/plot.STR.Rd | 127 - stR-0.3/stR/man/plotBeta.Rd |only stR-0.3/stR/man/predictors.Rd | 104 - stR-0.3/stR/man/reltol.Rd | 28 stR-0.3/stR/man/reportDimensionsOnly.Rd | 30 stR-0.3/stR/man/robust.Rd | 26 stR-0.3/stR/man/seasadj.STR.Rd | 70 stR-0.3/stR/man/solver.Rd | 33 stR-0.3/stR/man/strDesign.Rd | 30 stR-0.3/stR/man/trace.Rd | 26 stR-0.3/stR/tests/testthat.R | 8 stR-0.3/stR/tests/testthat/Rplots.pdf |binary stR-0.3/stR/tests/testthat/test_STR.R | 2048 +++++++++++------------ stR-0.3/stR/vignettes/calls.fit.RDS |only stR-0.3/stR/vignettes/co2.fit.stR.RDS |only stR-0.3/stR/vignettes/co2.fit.tbats.RDS |only stR-0.3/stR/vignettes/elec.fit.2.forecasting.RDS |only stR-0.3/stR/vignettes/elec.fit.RDS |only stR-0.3/stR/vignettes/elec.fit.forecasting.RDS |only stR-0.3/stR/vignettes/gr.fit.2.stR.RDS |only stR-0.3/stR/vignettes/gr.fit.stR.RDS |only stR-0.3/stR/vignettes/logGrOutl.stR.RDS |only stR-0.3/stR/vignettes/logGrOutl.stR.robust.RDS |only stR-0.3/stR/vignettes/stRvignette.Rmd | 427 +++- stR-0.3/stR/vignettes/taylor.fit.stR.RDS |only 68 files changed, 4413 insertions(+), 3295 deletions(-)
Title: Analytic Hierarchy Process
Description: Model and analyse complex decision making problems
using the Analytic Hierarchy Process (AHP) by Thomas Saaty.
Author: Christoph Glur
Maintainer: Christoph Glur <christoph.glur@ipub.com>
Diff between ahp versions 0.2.10 dated 2016-11-27 and 0.2.11 dated 2017-01-06
DESCRIPTION | 8 ++--- MD5 | 18 ++++++------ NAMESPACE | 6 ---- NEWS | 4 ++ R/gui.R | 7 +++- R/visualize.R | 57 ++++++++++++++++++++++++---------------- build/vignette.rds |binary inst/gui/shiny/server.R | 2 - man/RunGUI.Rd | 8 ++++- tests/testthat/test-Visualize.R | 6 ++-- 10 files changed, 68 insertions(+), 48 deletions(-)
Title: Unit Root Tests for Seasonal Time Series
Description: Seasonal unit roots and seasonal stability tests.
P-values based on response surface regressions are available for both tests.
P-values based on bootstrap are available for seasonal unit root tests.
A parallel implementation of the bootstrap method requires a CUDA capable GPU
with compute capability >= 3.0, otherwise a debugging version fully coded in R is used.
Author: Javier López-de-Lacalle <javlacalle@yahoo.es>
Maintainer: Javier López-de-Lacalle <javlacalle@yahoo.es>
Diff between uroot versions 2.0-5 dated 2016-03-19 and 2.0-6 dated 2017-01-06
uroot-2.0-5/uroot/src/uroot.cpp |only uroot-2.0-6/uroot/DESCRIPTION | 13 - uroot-2.0-6/uroot/MD5 | 18 +- uroot-2.0-6/uroot/NEWS | 14 +- uroot-2.0-6/uroot/R/hegy-rs-pvalue.R | 2 uroot-2.0-6/uroot/R/hegy-test.R.in | 2 uroot-2.0-6/uroot/cleanup |only uroot-2.0-6/uroot/configure | 187 ++++++++++++++++++++++------ uroot-2.0-6/uroot/configure.ac | 145 ++++++++++++++++++--- uroot-2.0-6/uroot/src/COMPILE_CUDA_FALSE.mk |only uroot-2.0-6/uroot/src/COMPILE_CUDA_TRUE.mk |only uroot-2.0-6/uroot/src/Makevars.in | 29 ---- 12 files changed, 308 insertions(+), 102 deletions(-)
Title: 'Semantic Versioning V2.0.0' Parser
Description: Tools and functions for parsing, rendering and operating on
semantic version strings. Semantic versioning is a simple set of rules
and requirements that dictate how version numbers are assigned and
incremented as outlined at <http://semver.org>.
Author: John Harrison [aut, cre] (R package semantic),
Marko Živanović [aut, cph] (semver cpp library,
https://github.com/zmarko/semver)
Maintainer: John Harrison <johndharrison0@gmail.com>
Diff between semver versions 0.1.0 dated 2017-01-02 and 0.2.0 dated 2017-01-06
DESCRIPTION | 8 - MD5 | 50 ++++--- NAMESPACE | 10 + NEWS.md | 29 ++++ R/RcppExports.R | 12 + R/assertions.R | 45 +++++++ R/increment_version.R |only R/reset_version.R |only R/semver_classes.R | 9 + R/set_version.R |only README.md | 6 inst/doc/basics.R | 85 +++++++++++++ inst/doc/basics.Rmd | 170 ++++++++++++++++++++++++++ inst/doc/basics.html | 204 ++++++++++++++++++++++++++++++-- man/increment_version.Rd |only man/reset_version.Rd |only man/set_version.Rd |only src/RcppExports.cpp | 49 ++++++- src/Semver200_comparator.cpp | 2 src/Semver200_modifier.cpp |only src/Semver200_parser.cpp | 2 src/semver200.h | 22 ++- src/semverR.cpp | 80 +++++++++++- src/semver_types.h | 14 +- src/version.h | 124 ++++++++++++++----- src/versioninl.h | 164 ++++++++++++++++++------- tests/testthat/test-increment_version.R |only tests/testthat/test-misc_tests.R | 3 tests/testthat/test-reset_version.R |only tests/testthat/test-set_version.R |only vignettes/basics.Rmd | 170 ++++++++++++++++++++++++++ 31 files changed, 1121 insertions(+), 137 deletions(-)
Title: A Simple R-Based Implementation of a Trie (A.k.a. Digital
Tree/Radix Tree/Prefix Tree)
Description: A simple R-based implementation of a Trie (a.k.a. digital tree/radix tree/prefix tree)
A trie, also called digital tree and sometimes radix tree or prefix tree is a kind of search tree.
This ordered tree data structure is used to store a dynamic set or associative array where the keys are usually strings.
Author: Casimir Saternos [aut, cre]
Maintainer: Casimir Saternos <cas.saternos@gmail.com>
Diff between rtrie versions 0.1.0 dated 2017-01-05 and 0.1.1 dated 2017-01-06
DESCRIPTION | 9 +++++---- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/trie_usage.Rmd | 2 +- inst/doc/trie_usage.html | 2 +- vignettes/trie_usage.Rmd | 2 +- 6 files changed, 13 insertions(+), 12 deletions(-)
Title: A Code Generator for ODE-Based Models
Description: Provides an R6 class and several utility methods to
facilitate the implementation of models based on ordinary
differential equations. The heart of the package is a code generator
that creates compiled 'Fortran' (or 'R') code which can be passed to
a numerical solver. There is direct support for solvers contained
in packages 'deSolve' and 'rootSolve'.
Author: David Kneis <david.kneis@tu-dresden.de>
Maintainer: David Kneis <david.kneis@tu-dresden.de>
Diff between rodeo versions 0.7 dated 2016-12-23 and 0.7.1 dated 2017-01-06
DESCRIPTION | 15 +++++++++------ MD5 | 16 ++++++++-------- R/classMethods_lib.r | 4 ++-- R/internal_functions.r | 10 ++++++---- inst/doc/rodeoVignette.Rmd | 6 +++--- inst/doc/rodeoVignette.pdf |binary man/libFunc.Rd | 1 + man/libName.Rd | 1 + vignettes/rodeoVignette.Rmd | 6 +++--- 9 files changed, 33 insertions(+), 26 deletions(-)
Title: Model Based Clustering, Classification and Discriminant Analysis
Using the Mixture of Generalized Hyperbolic Distributions
Description: Carries out model-based clustering, classification and discriminant analysis using five different models. The models are all based on the generalized hyperbolic distribution.The first model 'MGHD' is the classical mixture of generalized hyperbolic distributions. The 'MGHFA' is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The 'MSGHD', mixture of multiple scaled generalized hyperbolic distributions. The 'cMSGHD' is a 'MSGHD' with convex contour plots. The 'MCGHD', mixture of coalesced generalized hyperbolic distributions is a new more flexible model.
Author: Cristina Tortora, Aisha ElSherbiny, Ryan P. Browne, Brian C. Franczak, and Paul D. McNicholas.
Maintainer: Cristina Tortora <grikris1@gmail.com>
Diff between MixGHD versions 2.0 dated 2016-10-04 and 2.1 dated 2017-01-06
DESCRIPTION | 13 +++++++------ MD5 | 44 ++++++++++++++++++++++++-------------------- NAMESPACE | 7 ++++++- R/DA.R | 21 +++++++++++---------- R/GHD.R | 40 ++++++++++++++++++++++++++++++++++++++++ R/MCGHD.R | 15 ++++++++++----- R/MGHD.R | 13 +++++++++---- R/MGHFA.R | 7 +++++-- R/MSGHD.R | 11 +++++++---- R/cMSGHD.R | 8 ++++---- R/contourpl.R | 24 ++++++++++++------------ man/ARI.Rd | 4 ++-- man/DA.Rd | 15 ++++++++------- man/MCGHD.Rd | 11 ++++++----- man/MGHD.Rd | 12 ++++++------ man/MGHFA.Rd | 10 +++++----- man/MSGHD.Rd | 11 ++++++----- man/MixGHD-class.Rd |only man/MixGHD.Rd |only man/cMSGHD.Rd | 7 +++---- man/contourpl.Rd | 16 ++++------------ man/plot.MixGHD.Rd |only man/summary.MixGHD.Rd |only src/GHD.c | 2 +- src/zbsubs.c | 19 ++++++++++--------- 25 files changed, 186 insertions(+), 124 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from
several federated data sources (mainly sources maintained by the US Federal
government). Currently, the package allows for retrieval of five datasets:
The National Elevation Dataset digital elevation models (1 and 1/3 arc-second;
USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic
(SSURGO) database from the National Cooperative Soil Survey (NCSS), which is
led by the Natural Resources Conservation Service (NRCS) under the USDA; the
Global Historical Climatology Network (GHCN), coordinated by National Climatic
Data Center at NOAA; the Daymet gridded estimates of daily weather parameters
for North America, version 3, available from the Oak Ridge National Laboratory's
Distributed Active Archive Center (DAAC); and the International Tree Ring Data Bank.
Additional data sources are in the works, global soils (HWSD),
MODIS satellite data products, the National Atlas (US), Natural Earth, and WorldClim.
Author: R. Kyle Bocinsky [aut, cre], Dylan Beaudette [ctb], Scott Chamberlain [ctb]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 2.3.2 dated 2016-10-27 and 2.3.5 dated 2017-01-06
DESCRIPTION | 10 ++++---- MD5 | 16 +++++++------- R/GHCN_FUNCTIONS.R | 2 - R/NED_FUNCTIONS.R | 48 +++++++++++++++++++++++++++++++++++++------ R/SSURGO_FUNCTIONS.R | 29 ++++++++++++++++++------- README.md | 39 ++++++++++++++++++++++++---------- inst/FedDataTester.R | 32 ++++++++++++++-------------- man/FedData-package.Rd | 6 ++--- tests/testthat/test.SSURGO.R | 2 - 9 files changed, 124 insertions(+), 60 deletions(-)
Title: Extended HOF (Huisman-Olff-Fresco) Models
Description: Extended and enhanced hierarchical logistic regression models (called Huisman-Olff-Fresco in biology, see Huisman et al. 1993 JVS <doi:10.1111/jvs.12050>) models. Response curves along one-dimensional gradients including no response, monotone, plateau, unimodal and bimodal models.
Author: Florian Jansen, Jari Oksanen
Maintainer: Florian Jansen <jansen@uni-greifswald.de>
Diff between eHOF versions 1.7 dated 2016-03-14 and 1.8 dated 2017-01-06
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- R/HOF.data.frame.r | 1 - R/Para.niche.r | 17 ++++++++++------- R/Para.r | 6 ++++-- build/vignette.rds |binary inst/ChangeLog | 2 ++ inst/doc/eHOF.R | 3 --- inst/doc/eHOF.Rnw | 3 +-- inst/doc/eHOF.pdf |binary man/plot.HOF.Rd | 2 +- vignettes/eHOF.Rnw | 3 +-- 12 files changed, 35 insertions(+), 34 deletions(-)
Title: General Purpose Hierarchical Data Structure
Description: Create tree structures from hierarchical data, and traverse the
tree in various orders. Aggregate, cumulate, print, plot, convert to and from
data.frame and more. Useful for decision trees, machine learning, finance,
conversion from and to JSON, and many other applications.
Author: Facundo Munoz [ctb] (improve list conversion),
Markus Wamser [ctb] (fixed some typos),
Pierre Formont [ctb] (additional features),
Kent Russel [ctb] (documentation),
Noam Ross [ctb] (fixes),
Duncan Garmonsway [ctb] (fixes),
Christoph Glur [aut, cre] (R interface)
Maintainer: Christoph Glur <christoph.glur@ipub.com>
Diff between data.tree versions 0.6.2 dated 2016-11-24 and 0.7.0 dated 2017-01-06
data.tree-0.6.2/data.tree/man/ToGraphViz.Rd |only data.tree-0.7.0/data.tree/DESCRIPTION | 8 - data.tree-0.7.0/data.tree/MD5 | 22 +-- data.tree-0.7.0/data.tree/NAMESPACE | 2 data.tree-0.7.0/data.tree/NEWS | 6 data.tree-0.7.0/data.tree/R/node_conversion_igraph.R | 4 data.tree-0.7.0/data.tree/R/node_plot.R | 116 +++++++++---------- data.tree-0.7.0/data.tree/R/util.R | 2 data.tree-0.7.0/data.tree/inst/doc/applications.html | 65 +++++----- data.tree-0.7.0/data.tree/inst/doc/data.tree.html | 27 ++-- data.tree-0.7.0/data.tree/man/ToDiagrammeRGraph.Rd |only data.tree-0.7.0/data.tree/man/as.igraph.Node.Rd | 2 data.tree-0.7.0/data.tree/tests/testthat/test-draw.R | 108 ++++++++--------- 13 files changed, 186 insertions(+), 176 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-01-01 1.1.0
2015-07-08 1.0.5
2015-06-23 1.0.4
2015-06-08 1.0.3
2015-01-02 1.0.2
2014-11-03 1.0.1
2014-10-10 1.0.0
Title: Analyze Cricket Performances Based on Data from Cricsheet
Description: Analyzing performances of cricketers and cricket teams
based on 'yaml' match data from Cricsheet <http://cricsheet.org>.
Author: Tinniam V Ganesh
Maintainer: Tinniam V Ganesh <tvganesh.85@gmail.com>
Diff between yorkr versions 0.0.5 dated 2016-05-21 and 0.0.6 dated 2017-01-06
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/rankIPLBatsmen.R | 18 +++++++++++++----- R/rankIPLBowlers.R | 27 +++++++++++++++++++++++---- R/saveAllMatchesAllOppositionIPLT20.R | 12 ++++++++---- R/saveAllMatchesBetween2IPLTeams.R | 12 ++++++++---- README.md | 9 +++++++++ man/saveAllMatchesAllOppositionIPLT20.Rd | 5 ++++- man/saveAllMatchesBetween2IPLTeams.Rd | 5 ++++- 9 files changed, 81 insertions(+), 31 deletions(-)
Title: Streamlined Estimation of Survival for Static, Dynamic and
Stochastic Treatment and Monitoring Regimes
Description: Analysis of longitudinal time-to-event or time-to-failure data.
Estimates the counterfactual discrete survival curve under static, dynamic and
stochastic interventions on treatment (exposure) and monitoring events over time.
Estimators (IPW, MSM-IPW, GCOMP, longitudinal TMLE) adjust for measured time-varying
confounding and informative right-censoring. Model fitting can be performed either
with GLM or H2O-3 machine learning libraries.
The exposure, monitoring and censoring variables can be coded as either binary,
categorical or continuous. Each can be multivariate (e.g., can use more than one
column of dummy indicators for different censoring events).
The input data needs to be in long format.
Author: Oleg Sofrygin [aut, cre],
Mark J. van der Laan [aut],
Romain Neugebauer [aut]
Maintainer: Oleg Sofrygin <oleg.sofrygin@gmail.com>
Diff between stremr versions 0.2 dated 2016-10-03 and 0.4 dated 2017-01-06
stremr-0.2/stremr/man/h2o.glm_nn.Rd |only stremr-0.4/stremr/DESCRIPTION | 13 stremr-0.4/stremr/MD5 | 78 +-- stremr-0.4/stremr/NAMESPACE | 2 stremr-0.4/stremr/NEWS | 5 stremr-0.4/stremr/R/BinomialGLMsClass.R | 9 stremr-0.4/stremr/R/BinomialMLclass.R | 45 - stremr-0.4/stremr/R/BinomialModelClass.R | 7 stremr-0.4/stremr/R/DataStorageClass.R | 169 +----- stremr-0.4/stremr/R/QlearningClasses.R | 35 - stremr-0.4/stremr/R/SL.R | 121 ----- stremr-0.4/stremr/R/helper_routines.R | 36 + stremr-0.4/stremr/R/main_estimation.R | 10 stremr-0.4/stremr/R/reports.R | 107 +++- stremr-0.4/stremr/R/stremr.R | 9 stremr-0.4/stremr/R/tmle.R | 136 ++++- stremr-0.4/stremr/R/zzz.R | 6 stremr-0.4/stremr/README.md | 107 ---- stremr-0.4/stremr/inst/report/report-script-rmd.R | 119 +++- stremr-0.4/stremr/man/fitIterTMLE.Rd | 81 --- stremr-0.4/stremr/man/fitPropensity.Rd | 81 --- stremr-0.4/stremr/man/fitSeqGcomp.Rd | 101 ---- stremr-0.4/stremr/man/fitTMLE.Rd | 81 --- stremr-0.4/stremr/man/getIPWeights.Rd | 81 --- stremr-0.4/stremr/man/get_FUPtimes.Rd |only stremr-0.4/stremr/man/importData.Rd | 81 --- stremr-0.4/stremr/man/make_report_rmd.Rd | 21 stremr-0.4/stremr/man/survDirectIPW.Rd | 81 --- stremr-0.4/stremr/man/survNPMSM.Rd | 81 --- stremr-0.4/stremr/tests/RUnit/0_simulate_data_1.R | 4 stremr-0.4/stremr/tests/RUnit/0_simulate_data_2.R | 2 stremr-0.4/stremr/tests/RUnit/RUnit_tests_00.R | 6 stremr-0.4/stremr/tests/RUnit/RUnit_tests_04a_sims10K_speedglm.R | 65 ++ stremr-0.4/stremr/tests/RUnit/RUnit_tests_04b_sims10K_h2oGLM.R | 142 ++--- stremr-0.4/stremr/tests/RUnit/RUnit_tests_04c_sims10K_h2o_ALL_ML.R | 242 ++++------ stremr-0.4/stremr/tests/RUnit/RUnit_tests_04d_sims10K_tmle_speedglm.R | 2 stremr-0.4/stremr/tests/RUnit/RUnit_tests_05_stremr_example_SL.R | 198 -------- stremr-0.4/stremr/tests/RUnit/RUnit_tests_06_direct_regression_def.R | 161 ------ stremr-0.4/stremr/tests/RUnit/RUnit_tests_07_iterativeTMLE.R | 55 +- stremr-0.4/stremr/tests/RUnit/RUnit_tests_08_h2oQuasiBinomGLM.R | 159 +++--- stremr-0.4/stremr/tests/examples/2_building_blocks_example.R | 81 --- 41 files changed, 840 insertions(+), 1980 deletions(-)
Title: Sustainable Transport Planning
Description: Functionality and data access tools for transport planning,
including origin-destination analysis, route allocation and modelling travel
patterns.
Author: Robin Lovelace [aut, cre],
Richard Ellison [aut],
Barry Rowlingson [ctb] (Author of overline),
Nick Bearman [ctb] (Co-author of gclip),
Malcolm Morgan [ctb] (Co-author of angle_diff),
Nikolai Berkoff [ctb] (Co-author of line2route)
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between stplanr versions 0.1.7-2 dated 2016-12-28 and 0.1.7-3 dated 2017-01-06
DESCRIPTION | 11 +- MD5 | 45 +++++---- NAMESPACE | 1 NEWS.md | 9 + R/RcppExports.R | 4 R/SpatialLinesNetwork.R | 131 +++++++++++++++++++---------- R/catchmentArea.R | 2 build/vignette.rds |binary inst/doc/introducing-stplanr.R | 1 inst/doc/introducing-stplanr.Rmd | 1 inst/doc/introducing-stplanr.html | 20 ++-- inst/doc/stplanr-paper.Rmd | 2 man/SpatialLinesNetwork.Rd | 6 + man/calc_network_catchment.Rd | 2 man/find_network_nodes.Rd | 6 + man/plot-SpatialLinesNetwork-ANY-method.Rd | 6 + man/sln2points.Rd |only man/sum_network_routes.Rd | 17 +++ man/summary-SpatialLinesNetwork-method.Rd | 8 + man/weightfield.Rd | 8 + src/RcppExports.cpp | 7 - src/spatialnetworks.cpp | 6 - vignettes/introducing-stplanr.Rmd | 1 vignettes/stplanr-paper.Rmd | 2 24 files changed, 202 insertions(+), 94 deletions(-)
Title: 'Neuroconductor' Base Package with Helper Functions for 'nifti'
Objects
Description: Base package for 'Neuroconductor', which includes many helper functions
that interact with objects of class 'nifti', implemented by
package 'oro.nifti', for reading/writing and also other manipulation functions.
Author: John Muschelli <muschellij2@gmail.com>
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between neurobase versions 1.1.1.1 dated 2016-09-27 and 1.9.2 dated 2017-01-06
DESCRIPTION | 13 +- MD5 | 179 ++++++++++++++++++++++------------- NAMESPACE | 22 ++++ R/applyEmptyImageDimensions.R | 19 ++- R/breaker.R | 2 R/check_mask.R | 5 R/check_nifti.R | 62 ++++++++++-- R/checkimg.R | 18 +++ R/checknii.R | 18 +++ R/checkniigz.R | 15 ++ R/copyNIfTIHeader.R | 1 R/density.nifti.R |only R/dropEmptyImageDimensions.R | 5 R/fast_readnii.R |only R/finite_img.R | 16 ++- R/getEmptyImageDimensions.R | 23 ++-- R/hist.nifti.R |only R/images2matrix.R |only R/img_indices.R |only R/import_methods.R | 2 R/mask_img.R | 14 ++ R/mask_vals.R |only R/mean.nifti.R |only R/niftiarr.R | 13 +- R/ortho2.R | 56 ++++++++-- R/overlay2.R | 57 +++++++---- R/quantile.nifti.R |only R/randomize_mask.R |only R/readNIfTI2.R | 2 R/remake_img.R | 11 +- R/robust_window.R | 10 + R/same_dims.R | 1 R/writenii.R | 18 ++- build |only inst |only man/applyEmptyImageDimensions.Rd | 4 man/breaker.Rd | 1 man/check_mask.Rd | 5 man/check_mask_fail.Rd | 1 man/check_nifti-methods.Rd | 38 +++++-- man/check_outfile.Rd | 1 man/checkimg-methods.Rd | 8 - man/checknii-methods.Rd | 8 - man/checkniigz-methods.Rd | 8 - man/cog.Rd | 1 man/colorbar.Rd | 1 man/copyNIfTIHeader.Rd | 1 man/datatype.Rd | 1 man/density.nifti.Rd |only man/double_ortho.Rd | 1 man/dropEmptyImageDimensions.Rd | 1 man/fast_readnii.Rd |only man/file_imgext.Rd | 1 man/finite_img-methods.Rd | 9 - man/getEmptyImageDimensions.Rd | 3 man/hist.nifti.Rd |only man/images2matrix.Rd |only man/img_indices.Rd |only man/maskEmptyImageDimensions.Rd | 1 man/mask_img.Rd | 13 ++ man/mask_vals-methods.Rd |only man/mean.nifti.Rd |only man/multi_overlay.Rd | 6 - man/newnii.Rd | 1 man/niftiarr.Rd | 1 man/nii.stub.Rd | 1 man/ortho2.Rd | 6 - man/ortho_diff.Rd | 1 man/parse_img_ext.Rd | 1 man/quantile.nifti.Rd |only man/quantile_img.Rd | 1 man/randomize_mask.Rd |only man/readNIfTI2.Rd | 3 man/remake_img.Rd | 3 man/replace_dropped_dimensions.Rd | 1 man/rescale_img.Rd | 1 man/robust_window.Rd | 5 man/same_dims.Rd | 4 man/tempimg.Rd | 1 man/window_img.Rd | 1 man/writeNIfTI2.Rd | 8 - man/xyz.Rd | 1 man/zero_pad.Rd | 1 man/zlimmer.Rd | 1 man/zscore_img.Rd | 1 tests/testthat/test-mask_img.R |only tests/testthat/test-randomize_mask.R |only vignettes |only 88 files changed, 516 insertions(+), 222 deletions(-)
Title: Flexible Modelling Functions for Epidemiological Data Analysis
Description: Provides flexible model fitting used in epidemiological data
analysis by a unified model specification, along with some data manipulation
functions. This package covers fitting of variety models including Cox
regression models, linear regression models, Poisson regression models, logistic
models and others whose likelihood is expressed in negative binomial, gamma and
Weibull distributions.
Author: Kazutaka Doi [aut,cre],
Kei Sakabe [ctb],
Masataka Taruri [ctb]
Maintainer: Kazutaka Doi <kztkdi@gmail.com>
Diff between epifit versions 0.1.1 dated 2016-10-28 and 0.1.2 dated 2017-01-06
DESCRIPTION | 8 - MD5 | 18 +- NAMESPACE | 77 ++++++------ NEWS | 6 R/epifit-package.R | 3 R/epifit.R | 30 ++++ R/modules.R | 306 ++++++++++++++++++++++++++++++++++++++++++++++++++ R/strscan.R |only man/epifit-package.Rd | 73 ++++++----- man/epifit.Rd | 24 +++ man/strscan.Rd |only 11 files changed, 453 insertions(+), 92 deletions(-)
Title: Embeddable Cairo Graphics Device Driver
Description: This device uses Cairo and GTK to draw to the screen,
file (png, svg, pdf, and ps) or memory (arbitrary GdkDrawable
or Cairo context). The screen device may be embedded into RGtk2
interfaces and supports all interactive features of other graphics
devices, including getGraphicsEvent().
Author: Michael Lawrence
Maintainer: Michael Lawrence <michafla@gene.com>
Diff between cairoDevice versions 2.23 dated 2015-12-13 and 2.24 dated 2017-01-06
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/Makevars.in | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)