Title: The Unifed Distribution
Description: Probability functions and family for glm() of the unifed distribution (Quijano Xacur, 2018; <arXiv:1812.00251>).
Author: Oscar Alberto Quijano Xacur [aut,cre]
Maintainer: Oscar Alberto Quijano Xacur <oscar.quijano@use.startmail.com>
Diff between unifed versions 1.0 dated 2019-01-30 and 1.0.1 dated 2019-02-06
DESCRIPTION | 14 ++--- MD5 | 14 +++-- README.md | 16 +++--- build/vignette.rds |binary inst/doc/introduction_unifed.Rmd | 14 ++--- inst/doc/introduction_unifed.html | 101 ++++++++++++++++---------------------- src/unifed_kappa.c | 18 ++++-- tests |only 8 files changed, 86 insertions(+), 91 deletions(-)
Title: Approximate Bayesian Computations for Phylogenetic Comparative
Methods
Description: Fits by ABC, the parameters of a stochastic process modelling the phylogeny and evolution of a suite of traits following the tree. The user may define an arbitrary Markov process for the trait and phylogeny. Importantly, trait-dependent speciation models are handled and fitted to data. See K. Bartoszek, P. Lio' (2018) <arXiv:1812.03715>.
Author: Krzysztof Bartoszek <krzbar@protonmail.ch>, Pietro Lio'
Maintainer: Krzysztof Bartoszek <krzbar@protonmail.ch>
Diff between pcmabc versions 1.0.1 dated 2019-02-05 and 1.0.2 dated 2019-02-06
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/simtree.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
More information about insurancerating at CRAN
Permanent link
Title: GroundWater Spatiotemporal Data Analysis Tool (GWSDAT)
Description: Shiny application for the analysis of groundwater monitoring data, designed to work with simple time-series data for solute concentration and ground water elevation, but can also plot non-aqueous phase liquid (NAPL) thickness if required. Also provides the import of a site basemap in GIS shapefile format.
Author: Wayne W Jones <wayne.w.jones@shell.com>, Ludger Evers <ludger.evers@glasgow.ac.uk>, Andrej Aderhold <andrej.aderhold@protonmail.com>
Maintainer: Ludger Evers <ludger.evers@glasgow.ac.uk>
Diff between GWSDAT versions 3.0.1 dated 2018-06-19 and 3.0.3 dated 2019-02-06
DESCRIPTION | 14 +- MD5 | 21 ++-- R/launchApp.R | 2 R/plotSpatialImage.R | 254 +++++++++++++++++++++++---------------------------- R/processData.R | 7 - R/readData.R | 52 ++-------- R/server.R | 166 ++++++++++++++++++--------------- R/shapeFiles.R | 7 - R/ui.R | 20 +++- R/uiSpatialImage.R | 8 + R/uiTrendTable.R | 11 +- inst/www/logo.png |only 12 files changed, 271 insertions(+), 291 deletions(-)
Title: Interim Analysis of Operational Futility in Randomized Trials
with Time-to-Event Endpoints and Fixed Follow-Up
Description: Randomized clinical trials commonly follow participants for a time-to-event efficacy endpoint for a fixed period of time. Consequently, at the time when the last enrolled participant completes their follow-up, the number of observed endpoints is a random variable. Assuming data collected through an interim timepoint, simulation-based estimation and inferential procedures in the standard right-censored failure time analysis framework are conducted for the distribution of the number of endpoints--in total as well as by treatment arm--at the end of the follow-up period. The future (i.e., yet unobserved) enrollment, endpoint, and dropout times are generated according to mechanisms specified in the simTrial() function in the 'seqDesign' package. A Bayesian model for the endpoint rate, offering the option to specify a robust mixture prior distribution, is used for generating future data (see the vignette for details). Inference can be restricted to participants who received treatment according to the protocol and are observed to be at risk for the endpoint at a specified timepoint. Plotting functions are provided for graphical display of results.
Author: Yingying Zhuang [aut],
Michal Juraska [aut, cre],
Doug Grove [ctb],
Peter Gilbert [ctb],
Alexander Luedtke [ctb],
Sanne Roels [ctb],
An Vandebosch [ctb]
Maintainer: Michal Juraska <mjuraska@fredhutch.org>
Diff between futility versions 0.2 dated 2017-11-22 and 0.3 dated 2019-02-06
DESCRIPTION | 26 + MD5 | 23 - R/futility.R | 519 +++++++++++++++++-------------- README.md |only build/vignette.rds |binary inst/doc/bayesianIncidenceRateModel.Rnw | 4 inst/doc/bayesianIncidenceRateModel.pdf |binary man/completeTrial.byArm.Rd | 22 - man/completeTrial.pooledArms.Rd | 17 - man/plotRCDF.byArm.Rd | 14 man/plotRCDF.pooledArms.Rd | 9 vignettes/bayesianIncidenceRateModel.Rnw | 4 vignettes/references.bib | 80 ++-- 13 files changed, 404 insertions(+), 314 deletions(-)
Title: Interface to 'ECMWF' and 'CDS' Data Web Services
Description: Programmatic interface to the European Centre for Medium-Range
Weather Forecasts public and restricted dataset web services (ECMWF;
<https://www.ecmwf.int/>) as well as Copernicus's Climate Data Store (CDS;
<https://cds.climate.copernicus.eu>). Allows for easy downloads of weather
forecasts and climate data directly to your R work space or your computer.
Author: Koen Hufkens [aut, cre],
Reto Stauffer [ctb] (<https://orcid.org/0000-0002-3798-5507>)
Maintainer: Koen Hufkens <koen.hufkens@gmail.com>
Diff between ecmwfr versions 1.0.1 dated 2019-01-19 and 1.1.0 dated 2019-02-06
ecmwfr-1.0.1/ecmwfr/inst/doc/ecmwfr_vignette.R |only ecmwfr-1.0.1/ecmwfr/inst/doc/ecmwfr_vignette.Rmd |only ecmwfr-1.0.1/ecmwfr/inst/doc/ecmwfr_vignette.html |only ecmwfr-1.0.1/ecmwfr/tests/testthat/test_main_functions.r |only ecmwfr-1.0.1/ecmwfr/vignettes/ecmwfr_vignette.Rmd |only ecmwfr-1.1.0/ecmwfr/DESCRIPTION | 40 +- ecmwfr-1.1.0/ecmwfr/MD5 | 61 ++-- ecmwfr-1.1.0/ecmwfr/NAMESPACE | 3 ecmwfr-1.1.0/ecmwfr/R/wf_check_request.R |only ecmwfr-1.1.0/ecmwfr/R/wf_datasets.R | 53 ++- ecmwfr-1.1.0/ecmwfr/R/wf_delete.R | 52 ++- ecmwfr-1.1.0/ecmwfr/R/wf_get_key.R | 14 ecmwfr-1.1.0/ecmwfr/R/wf_product_info.R |only ecmwfr-1.1.0/ecmwfr/R/wf_request.R | 217 +++++++++------ ecmwfr-1.1.0/ecmwfr/R/wf_services.R | 21 - ecmwfr-1.1.0/ecmwfr/R/wf_set_key.R | 13 ecmwfr-1.1.0/ecmwfr/R/wf_transfer.R | 113 +++++-- ecmwfr-1.1.0/ecmwfr/R/wf_user_info.R | 26 - ecmwfr-1.1.0/ecmwfr/R/zzz.R | 103 ++++++- ecmwfr-1.1.0/ecmwfr/build/vignette.rds |binary ecmwfr-1.1.0/ecmwfr/inst/doc/cds_vignette.R |only ecmwfr-1.1.0/ecmwfr/inst/doc/cds_vignette.Rmd |only ecmwfr-1.1.0/ecmwfr/inst/doc/cds_vignette.html |only ecmwfr-1.1.0/ecmwfr/inst/doc/webapi_vignette.R |only ecmwfr-1.1.0/ecmwfr/inst/doc/webapi_vignette.Rmd |only ecmwfr-1.1.0/ecmwfr/inst/doc/webapi_vignette.html |only ecmwfr-1.1.0/ecmwfr/inst/extdata |only ecmwfr-1.1.0/ecmwfr/man/wf_check_request.Rd |only ecmwfr-1.1.0/ecmwfr/man/wf_datasets.Rd | 12 ecmwfr-1.1.0/ecmwfr/man/wf_delete.Rd | 10 ecmwfr-1.1.0/ecmwfr/man/wf_get_key.Rd | 13 ecmwfr-1.1.0/ecmwfr/man/wf_product_info.Rd |only ecmwfr-1.1.0/ecmwfr/man/wf_request.Rd | 47 ++- ecmwfr-1.1.0/ecmwfr/man/wf_services.Rd | 8 ecmwfr-1.1.0/ecmwfr/man/wf_set_key.Rd | 11 ecmwfr-1.1.0/ecmwfr/man/wf_transfer.Rd | 20 + ecmwfr-1.1.0/ecmwfr/man/wf_user_info.Rd | 10 ecmwfr-1.1.0/ecmwfr/tests/testthat/test_cds.R |only ecmwfr-1.1.0/ecmwfr/tests/testthat/test_ecmwf.r |only ecmwfr-1.1.0/ecmwfr/vignettes/cds_vignette.Rmd |only ecmwfr-1.1.0/ecmwfr/vignettes/webapi_vignette.Rmd |only 41 files changed, 579 insertions(+), 268 deletions(-)
Title: Randomer Forest
Description: R-RerF (aka Randomer Forest (RerF) or Random Projection
Forests) is an algorithm developed by Tomita (2016) <arXiv:1506.03410v2>
which is similar to Random Forest - Random Combination (Forest-RC)
developed by Breiman (2001) <doi:10.1023/A:1010933404324>. Random
Forests create axis-parallel, or orthogonal trees. That is, the feature
space is recursively split along directions parallel to the axes of the
feature space. Thus, in cases in which the classes seem inseparable
along any single dimension, Random Forests may be suboptimal. To
address this, Breiman also proposed and characterized Forest-RC, which
uses linear combinations of coordinates rather than individual
coordinates, to split along. This package, 'rerf', implements RerF
which is similar to Forest-RC. The difference between the two
algorithms is where the random linear combinations occur: Forest-RC
combines features at the per tree level whereas RerF takes linear
combinations of coordinates at every node in the tree.
Author: Jesse Patsolic [ctb, cre],
Benjamin Falk [ctb],
Jaewon Chung [ctb],
James Browne [aut],
Tyler Tomita [aut],
Joshua Vogelstein [ths]
Maintainer: Jesse Patsolic <software@neurodata.io>
Diff between rerf versions 2.0.2 dated 2018-12-04 and 2.0.3 dated 2019-02-06
DESCRIPTION | 12 +- MD5 | 53 +++++---- NAMESPACE | 5 NEWS.md | 22 +++ R/BuildTree.R | 15 -- R/FeatureImportance.R | 108 +++++++++++++++++-- R/PrintTree.R |only R/RandMat.R | 41 ++++++- R/RerF.R | 1 R/RunFeatureImportance.R | 76 +++++++++++++ R/RunPredict.R | 3 R/Urerf.R | 23 +++- R/UrerfHelperFunctions.R | 177 +++++++++++++++++++++++++++++++- R/helperFunctions.R |only README.md | 87 ++++++++------- data/mnist.RData |binary man/BICCutFast.Rd |only man/BICCutMclust.Rd |only man/FeatureImportance.Rd | 32 +++++ man/GrowUnsupervisedForest.Rd | 6 - man/PrintTree.Rd |only man/RunFeatureImportanceBinary.Rd |only man/RunFeatureImportanceCounts.Rd |only man/Urerf.Rd | 14 ++ man/flipWeights.Rd |only man/getFeatures.Rd |only man/getWeights.Rd |only man/makeA.Rd |only man/makeAB.Rd | 5 man/uniqueByEquivalenceClass.Rd |only src/split.cpp | 5 tests/testthat/test-FeatureImportance.R |only tests/testthat/test-RandMat.R | 33 +++++ tests/testthat/test-predictions.R | 2 34 files changed, 600 insertions(+), 120 deletions(-)
Title: Spatial Temporal Aggregated Predictor Models via 'stan'
Description: Estimates previously compiled stap regression models using the 'rstan' package. Users specify models via a custom R syntax with a formula and data.frame plus additional arguments for priors.
Author: Adam Peterson [aut, cre]
Maintainer: Adam Peterson <atpvyc@umich.edu>
Diff between rstap versions 1.0.2 dated 2019-01-02 and 1.0.3 dated 2019-02-06
rstap-1.0.2/rstap/inst/include/csr_matrix_times_vector2.hpp |only rstap-1.0.3/rstap/DESCRIPTION | 6 +-- rstap-1.0.3/rstap/MD5 | 18 +++++----- rstap-1.0.3/rstap/inst/include/hello_world.hpp |only rstap-1.0.3/rstap/tests/testthat/test_methods.R | 2 - rstap-1.0.3/rstap/tools/make_cc.R | 3 - rstap-1.0.3/rstap/vignettes/Introduction_cache/html/__packages | 6 --- rstap-1.0.3/rstap/vignettes/Introduction_cache/html/sampling_1_4ad1d7f6ff35640ed3c0ba95c29a73f9.RData |binary rstap-1.0.3/rstap/vignettes/Introduction_cache/html/sampling_2_165e5eb59360b8617ee93e530dccf69d.RData |binary rstap-1.0.3/rstap/vignettes/Introduction_cache/html/sampling_3_2522ad175d8d8251040a9200ab32821f.RData |binary rstap-1.0.3/rstap/vignettes/Introduction_cache/html/sampling_4_15916be368dc126c01f40f04df59727f.RData |binary 11 files changed, 14 insertions(+), 21 deletions(-)
Title: Utility Functions for Exploratory Factor Analysis
Description: A number of utility function for exploratory factor analysis
are included in this package. In particular, it computes standard errors for
parameter estimates and factor correlations under a variety of conditions.
Author: Guangjian Zhang, Ge Jiang, Minami Hattori, Lauren Trichtinger
Maintainer: Guangjian Zhang <gzhang3@nd.edu>
Diff between EFAutilities versions 1.2.3 dated 2018-10-09 and 2.0.0 dated 2019-02-06
EFAutilities-1.2.3/EFAutilities/R/CIs20171005_c.R |only EFAutilities-1.2.3/EFAutilities/R/CompareSolutions20170808.R |only EFAutilities-1.2.3/EFAutilities/R/EFAEstimation20180511_c.R |only EFAutilities-1.2.3/EFAutilities/R/ModelTest20170816_c.R |only EFAutilities-1.2.3/EFAutilities/R/MultRandRotation20170808.R |only EFAutilities-1.2.3/EFAutilities/R/OblqDerivatives20171128_c.R |only EFAutilities-1.2.3/EFAutilities/R/OrthDerivatives20161103_c.R |only EFAutilities-1.2.3/EFAutilities/R/efa20181005_c.R |only EFAutilities-1.2.3/EFAutilities/R/efaMR20170811.R |only EFAutilities-1.2.3/EFAutilities/R/oblqSE20171128_c.R |only EFAutilities-1.2.3/EFAutilities/R/orthSE20170327_c.R |only EFAutilities-2.0.0/EFAutilities/DESCRIPTION | 10 EFAutilities-2.0.0/EFAutilities/MD5 | 47 - EFAutilities-2.0.0/EFAutilities/NAMESPACE | 2 EFAutilities-2.0.0/EFAutilities/NEWS.md | 5 EFAutilities-2.0.0/EFAutilities/R/CIs20181212_c.R |only EFAutilities-2.0.0/EFAutilities/R/CompareSolutions20190124_c.R |only EFAutilities-2.0.0/EFAutilities/R/EFAEstimation20181209_c.R |only EFAutilities-2.0.0/EFAutilities/R/ESEMpstQ20180816_c.R |only EFAutilities-2.0.0/EFAutilities/R/ModelTest20181231_c.R |only EFAutilities-2.0.0/EFAutilities/R/MultRandRotation20190126_2_c.R |only EFAutilities-2.0.0/EFAutilities/R/OblqDerivatives20181211_c.R |only EFAutilities-2.0.0/EFAutilities/R/OrthDerivatives20181210_c.R |only EFAutilities-2.0.0/EFAutilities/R/PolycorGamma20161107_c.R | 2 EFAutilities-2.0.0/EFAutilities/R/efa20190119_c.R |only EFAutilities-2.0.0/EFAutilities/R/efaMR20190129_c.R |only EFAutilities-2.0.0/EFAutilities/R/oblqSE20181210_c.R |only EFAutilities-2.0.0/EFAutilities/R/orthSE20181210_c.R |only EFAutilities-2.0.0/EFAutilities/R/ssem20190120_c.R |only EFAutilities-2.0.0/EFAutilities/R/ssemSE20181212_c.R |only EFAutilities-2.0.0/EFAutilities/build |only EFAutilities-2.0.0/EFAutilities/inst |only EFAutilities-2.0.0/EFAutilities/man/Align.Matrix.Rd | 3 EFAutilities-2.0.0/EFAutilities/man/BFI228.rd | 2 EFAutilities-2.0.0/EFAutilities/man/efa.Rd | 469 +++++----- EFAutilities-2.0.0/EFAutilities/man/efaMR.Rd | 235 ++--- EFAutilities-2.0.0/EFAutilities/man/ssem.Rd |only EFAutilities-2.0.0/EFAutilities/vignettes |only 38 files changed, 407 insertions(+), 368 deletions(-)
Title: Tools for CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable observing of the climate
system by providing essential climate variables related to the energy and water
cycle of the atmosphere (<http://www.cmsaf.eu>). It is a joint cooperation of seven
National Meteorological and Hydrological Services.
The 'cmsaf' R-package provides a collection of R-operators for the analysis and
manipulation of CM SAF NetCDF formatted data. The 'cmsaf' R-package is tested
for CM SAF NetCDF data, which are structured in three-dimensional arrays
(longitude, latitude, time) on a rectangular grid. Layered CM SAF data have to
be converted with the provided levbox_mergetime() function. The 'cmsaf' R-package
operators have only minor checks for deviations from the recommended data structure,
and give only few specific error messages.
Scripts for an easy application of the 'cmsaf' package operators and the preparation
and visualization of CM SAF NetCDF data are provided at the CM SAF webpage
(<http://www.cmsaf.eu/EN/Products/Tools/Tools_node.html>).
Author: Steffen Kothe <Steffen.Kothe@dwd.de>
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsaf versions 1.9.4 dated 2018-08-06 and 1.9.5 dated 2019-02-06
DESCRIPTION | 8 MD5 | 26 - NAMESPACE | 1 R/box_mergetime.R | 735 +++++++++++++++++++++++++-------------------------- R/cmsaf.cat.R | 692 ++++++++++++++++++++++++------------------------ R/levbox_mergetime.R | 718 +++++++++++++++++++++++++------------------------ R/seas.anomaly.R | 117 ++++---- R/seasmean.R | 71 ++-- R/seassum.R |only R/timmean.R | 12 R/timsum.R | 12 man/cmsaf-package.Rd | 4 man/seassum.Rd |only man/timmean.Rd | 5 man/timsum.Rd | 5 15 files changed, 1231 insertions(+), 1175 deletions(-)
Title: Download Mexico City Pollution, Wind, and Temperature Data
Description: Tools for downloading hourly averages, daily maximums and minimums from each of the
pollution, wind, and temperature measuring stations or geographic zones in the Mexico City
metro area. The package also includes the locations of each of the stations and zones. See
<http://aire.cdmx.gob.mx/> for more information.
Author: Diego Valle-Jones [aut, cre]
Maintainer: Diego Valle-Jones <diego@diegovalle.net>
Diff between aire.zmvm versions 0.8.0 dated 2018-10-30 and 0.8.1 dated 2019-02-06
DESCRIPTION | 6 - MD5 | 24 +++--- NEWS.md | 8 ++ R/convert_to_imeca.R | 93 ++++++++++++++------------- R/convert_to_index.R | 8 -- R/get_latest_imeca.R | 90 ++++++++++++++------------ R/get_zone_imeca.R | 66 ++++++++++--------- man/convert_to_imeca.Rd | 7 -- tests/testthat/test_convert_to_imeca.R | 20 ++--- tests/testthat/test_convert_to_index.R | 6 - tests/testthat/test_download_archives.R | 4 - tests/testthat/test_get_station_data.R | 14 ++-- tests/testthat/test_get_station_month_data.R | 10 +- 13 files changed, 192 insertions(+), 164 deletions(-)
Title: Principal Tensor Analysis on k Modes
Description: A multiway method to decompose a tensor (array) of any order, as a generalisation of SVD also supporting non-identity metrics and penalisations. 2-way SVD with these extensions is also available. The package includes also some other multiway methods: PCAn (Tucker-n) and PARAFAC/CANDECOMP with these extensions.
Author: Leibovici & Sabatier (1998) <doi:10.1016/S0024-3795(97)81516-9>, Didier G. Leibovici (2010)<doi:10.18637/jss.v034.i10>
Maintainer: Didier G. Leibovici <GeotRYcs@gmail.com>
Diff between PTAk versions 1.2-12 dated 2015-07-20 and 1.3-34 dated 2019-02-06
DESCRIPTION | 14 - MD5 | 58 ++--- R/PTAk.R | 541 ++++++++++++++++++++++++++++++----------------- inst/CITATION | 14 - inst/doc/PTAkgeneral.pdf |binary inst/doc/PTAklogo.png |binary inst/doc/index.html | 88 +++---- man/APSOLU3.Rd | 2 man/APSOLUk.Rd | 4 man/CANDPARA.Rd | 3 man/CONTRACTION.Rd | 2 man/COS2CTR.PTAk.Rd | 64 +++++ man/CauRuimet.Rd | 2 man/FCA2.Rd | 3 man/FCAk.Rd | 3 man/FCAmet.Rd | 3 man/INITIA.Rd | 9 man/PCAn.Rd | 4 man/PROJOT.Rd | 5 man/PTA3.Rd | 2 man/PTAk-internal.Rd | 7 man/PTAk.Rd | 2 man/REBUILD.Rd | 2 man/SINGVA.Rd | 4 man/SVDgen.Rd | 2 man/TENSELE.Rd | 2 man/howtoPTAk.Rd | 8 man/plot.PTAk.Rd | 8 man/preprocessings.Rd | 3 man/summary.PTAk.Rd | 2 30 files changed, 545 insertions(+), 316 deletions(-)
Title: Estimating Parameters for a Matched Case Control Design with a
Mismeasured Exposure using Instrumental Variables
Description: Applying the methodology from Manuel et al., estimates for the
parameters for matched case control data with a mismeasured exposure are calculated
through the use of user supplied instrumental variables (Submitted).
Author: Chris M Manuel, Samiran Sinha, and Suojin Wang
Maintainer: Chris M Manuel <cmmanuel@stat.tamu.edu>
Diff between mccmeiv versions 1.1 dated 2018-09-12 and 2.0 dated 2019-02-06
mccmeiv-1.1/mccmeiv/R/functions.r |only mccmeiv-1.1/mccmeiv/R/main.r |only mccmeiv-1.1/mccmeiv/R/nlglik2_no_z.r |only mccmeiv-1.1/mccmeiv/R/stderr1_no_z.r |only mccmeiv-1.1/mccmeiv/R/stderr2_no_z.r |only mccmeiv-1.1/mccmeiv/data/matcdata2.RData |only mccmeiv-1.1/mccmeiv/man/matcdata2.Rd |only mccmeiv-1.1/mccmeiv/man/meiv.Rd |only mccmeiv-2.0/mccmeiv/DESCRIPTION | 19 - mccmeiv-2.0/mccmeiv/MD5 | 51 +- mccmeiv-2.0/mccmeiv/NAMESPACE | 25 - mccmeiv-2.0/mccmeiv/R/meivm3.r |only mccmeiv-2.0/mccmeiv/R/meivm4.r |only mccmeiv-2.0/mccmeiv/R/method4.r |only mccmeiv-2.0/mccmeiv/R/method4noa0.r |only mccmeiv-2.0/mccmeiv/R/method4noa1.r |only mccmeiv-2.0/mccmeiv/R/nlglik1.r | 517 +--------------------------- mccmeiv-2.0/mccmeiv/R/nlglik1noa0.r |only mccmeiv-2.0/mccmeiv/R/nlglik1noa1.r |only mccmeiv-2.0/mccmeiv/R/nlglik2.r | 147 ------- mccmeiv-2.0/mccmeiv/R/nlglik2noa0.r |only mccmeiv-2.0/mccmeiv/R/nlglik2noa1.r |only mccmeiv-2.0/mccmeiv/R/output.r | 34 + mccmeiv-2.0/mccmeiv/R/outputnoa0.r |only mccmeiv-2.0/mccmeiv/R/outputnoa1.r |only mccmeiv-2.0/mccmeiv/R/stderr1.r | 74 +--- mccmeiv-2.0/mccmeiv/R/stderr1noa0.r |only mccmeiv-2.0/mccmeiv/R/stderr1noa1.r |only mccmeiv-2.0/mccmeiv/R/stderr2.r | 247 ++++--------- mccmeiv-2.0/mccmeiv/R/stderr2noa0.r |only mccmeiv-2.0/mccmeiv/R/stderr2noa1.r |only mccmeiv-2.0/mccmeiv/build/partial.rdb |binary mccmeiv-2.0/mccmeiv/data/matcdata.RData |binary mccmeiv-2.0/mccmeiv/data/matcdatamult.RData |binary mccmeiv-2.0/mccmeiv/man/matcdata.Rd | 8 mccmeiv-2.0/mccmeiv/man/matcdatamult.Rd | 8 mccmeiv-2.0/mccmeiv/man/mccmeiv-package.Rd | 21 - mccmeiv-2.0/mccmeiv/man/meivm3.Rd |only mccmeiv-2.0/mccmeiv/man/meivm4.Rd |only 39 files changed, 235 insertions(+), 916 deletions(-)
Title: Printing Floating Point Numbers in a Human-Friendly Format
Description: Print vectors (and data frames) of floating point numbers
using a non-scientific format optimized for human readers. Vectors
of numbers are rounded using significant digits, aligned at the
decimal point, and all zeros trailing the decimal point are dropped.
See: Wright (2016). Lucid: An R Package for Pretty-Printing Floating Point
Numbers. In JSM Proceedings, Statistical Computing Section. Alexandria,
VA: American Statistical Association. 2270-2279.
Author: Kevin Wright [aut, cre] (<https://orcid.org/0000-0002-0617-8673>)
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between lucid versions 1.6 dated 2018-08-24 and 1.7 dated 2019-02-06
lucid-1.6/lucid/data/antibiotic.txt |only lucid-1.7/lucid/DESCRIPTION | 8 lucid-1.7/lucid/MD5 | 19 - lucid-1.7/lucid/NEWS.md |only lucid-1.7/lucid/R/lucid.R | 2 lucid-1.7/lucid/build/vignette.rds |binary lucid-1.7/lucid/data/antibiotic.txt.gz |only lucid-1.7/lucid/inst/doc/lucid_examples.Rmd | 95 +---- lucid-1.7/lucid/inst/doc/lucid_examples.html | 505 +++++++++++++++++++-------- lucid-1.7/lucid/tests/testthat/test_vc.R | 51 +- lucid-1.7/lucid/vignettes/lucid.bib | 3 lucid-1.7/lucid/vignettes/lucid_examples.Rmd | 95 +---- 12 files changed, 460 insertions(+), 318 deletions(-)
Title: Extract Decennial Census and American Community Survey Data
Description: Download summary files from Census Bureau <https://www2.census.gov/>
and extract data, in particular high resolution data at
block, block group, and tract level, from decennial census and
American Community Survey 1-year and 5-year estimates.
Author: Guanglai Li
Maintainer: Guanglai Li <liguanglai@gmail.com>
Diff between totalcensus versions 0.5.1 dated 2018-12-08 and 0.6.1 dated 2019-02-06
DESCRIPTION | 10 - MD5 | 34 ++-- R/convert_fips_and_names.R | 28 ---- R/download_census.R | 4 R/generate_data_from_census2010.R | 36 ++++- R/quiet_global_variable_in_cran_check.R | 3 R/read_acs1year.R | 58 ++++++-- R/read_acs5year.R | 67 +++++++-- R/read_decennial.R | 160 ++++++++++++++-------- R/search_census_and_acs.R | 7 - R/utilities.R | 224 ++++++++++++++++++++++++++++++++ man/convert_fips_to_names.Rd | 28 ---- man/dict_all_geocomponent_2000.Rd | 3 man/dict_all_geocomponent_2010.Rd | 3 man/search_geocomponents.Rd | 5 man/search_geoheaders.Rd | 2 man/search_summarylevels.Rd | 3 man/search_tablecontents.Rd | 6 18 files changed, 482 insertions(+), 199 deletions(-)
Title: Mixed GAM Computation Vehicle with Automatic Smoothness
Estimation
Description: Generalized additive (mixed) models, some of their extensions and
other generalized ridge regression with multiple smoothing
parameter estimation by (Restricted) Marginal Likelihood,
Generalized Cross Validation and similar, or using iterated
nested Laplace approximation for fully Bayesian inference. See
Wood (2017) <doi:10.1201/9781315370279> for an overview.
Includes a gam() function, a wide variety of smoothers, 'JAGS'
support and distributions beyond the exponential family.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between mgcv versions 1.8-26 dated 2018-11-21 and 1.8-27 dated 2019-02-06
ChangeLog | 35 +++++++ DESCRIPTION | 18 ++-- MD5 | 58 ++++++------- NAMESPACE | 11 +- R/bam.r | 58 +++++++------ R/coxph.r | 24 ++++- R/efam.r | 21 +++- R/fast-REML.r | 27 ------ R/gam.fit3.r | 19 ++-- R/gam.fit4.r | 50 ++++++----- R/gamlss.r | 231 ++++++++++++++++++++++++++++++++++++++++++++++++++-- R/inla.r |only R/mgcv.r | 46 ++++++++-- R/misc.r | 13 ++ R/mvam.r | 50 +++++++++-- R/smooth.r | 2 man/FFdes.Rd |only man/bam.Rd | 2 man/chol.down.Rd | 33 ++++++- man/coxph.Rd | 4 man/coxpht.Rd | 4 man/gam.Rd | 2 man/ginla.Rd |only man/mgcv-package.Rd | 2 man/plot.gam.Rd | 3 man/sp.vcov.Rd | 15 ++- man/twlss.Rd |only src/coxph.c | 2 src/init.c | 3 src/mat.c | 104 ++++++++++++++++++++++- src/mgcv.h | 1 tests/coxpht.R | 2 32 files changed, 665 insertions(+), 175 deletions(-)
Title: Bias Reduction in Generalized Linear Models
Description: Estimation and inference from generalized linear models based on various methods for bias reduction. The 'brglmFit' fitting method can achieve reduction of estimation bias by solving either the mean bias-reducing adjusted score equations in Firth (1993) <doi:10.1093/biomet/80.1.27> and Kosmidis and Firth (2009) <doi:10.1093/biomet/asp055>, or the median bias-reduction adjusted score equations in Kenne et al. (2016) <arXiv:1604.04768>, or through the direct subtraction of an estimate of the bias of the maximum likelihood estimator from the maximum likelihood estimates as in Cordeiro and McCullagh (1991) <http://www.jstor.org/stable/2345592>. Estimation in all cases takes place via a quasi Fisher scoring algorithm, and S3 methods for the construction of of confidence intervals for the reduced-bias estimates are provided. In the special case of generalized linear models for binomial and multinomial responses (both ordinal and nominal), the adjusted score approaches return estimates with improved frequentist properties, that are also always finite, even in cases where the maximum likelihood estimates are infinite (e.g. complete and quasi-complete separation). 'brglm2' also provides pre-fit and post-fit methods for detecting separation and infinite maximum likelihood estimates in binomial response generalized linear models.
Author: Ioannis Kosmidis [aut, cre],
Kjell Konis [ctb],
Euloge Clovis Kenne Pagui [ctb],
Nicola Sartori [ctb]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between brglm2 versions 0.1.8 dated 2018-04-16 and 0.5.0 dated 2019-02-06
DESCRIPTION | 15 +- MD5 | 88 +++++++++------ NAMESPACE | 13 ++ NEWS.md | 30 ++++- R/bracl.R |only R/brglm2-package.R | 9 - R/brglmControl.R | 20 +-- R/brglmFit.R | 123 +++++++++++++++------- R/brmultinom.R | 199 ++++++++++++++++++++++++++++++------ R/check_infinite_estimates.R | 6 - R/data.R | 36 ++++++ R/detect_separation.R | 18 +-- R/mis-link.R |only R/separator.R | 2 R/utils.R | 2 R/zzz_conventions.R | 12 ++ build/vignette.rds |binary data/stemcell.rda |only inst/CITATION |only inst/doc/adjacent.R |only inst/doc/adjacent.Rmd |only inst/doc/adjacent.html |only inst/doc/iteration.R | 3 inst/doc/iteration.Rmd | 5 inst/doc/iteration.html | 196 +++++++++-------------------------- inst/doc/multinomial.R | 3 inst/doc/multinomial.Rmd | 9 - inst/doc/multinomial.html | 153 ++++++++++++--------------- inst/doc/separation.R | 3 inst/doc/separation.Rmd | 5 inst/doc/separation.html | 64 +++-------- man/bracl.Rd |only man/brglmControl.Rd | 24 ++-- man/brglmFit.Rd | 36 ++++-- man/brmultinom.Rd | 21 +++ man/check_infinite_estimates.Rd | 4 man/check_infinite_estimates.glm.Rd | 4 man/detect_separation.Rd | 21 ++- man/detect_separation_control.Rd | 11 + man/endometrial.Rd | 2 man/mis.Rd |only man/predict.bracl.Rd |only man/predict.brmultinom.Rd |only man/residuals.brmultinom.Rd |only man/stemcell.Rd |only man/summary.brglmFit.Rd | 4 man/vcov.brglmFit.Rd | 8 - vignettes/adjacent.Rmd |only vignettes/brglm2.bib | 30 ++++- vignettes/iteration.Rmd | 5 vignettes/multinomial.Rmd | 9 - vignettes/separation.Rmd | 5 52 files changed, 690 insertions(+), 508 deletions(-)
Title: Client for the 'Alteryx Promote' API
Description: Deploy, maintain, and invoke predictive models using the 'Alteryx
Promote' REST API. 'Alteryx Promote' is available at the URL:
<https://www.alteryx.com/products/alteryx-promote>.
Author: Paul E. Promote <promotedev@alteryx.com>
Maintainer: Paul E. Promote <promotedev@alteryx.com>
Diff between promote versions 1.1.0 dated 2018-11-07 and 1.1.1 dated 2019-02-06
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/deps.R | 25 ++++--------------------- R/promote.R | 11 +++++++++-- man/add.dependency.Rd | 5 ++++- man/promote.library.Rd | 6 +++++- 6 files changed, 31 insertions(+), 34 deletions(-)
Title: Meta-Analysis of Significance Values
Description: The canonical way to perform meta-analysis involves using effect sizes.
When they are not available this package provides a number of methods for
meta-analysis of significance values including the methods of Edgington, Fisher,
Lancaster, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate published results;
and a routine for graphical display.
Author: Michael Dewey
Maintainer: Michael Dewey <lists@dewey.myzen.co.uk>
Diff between metap versions 1.0 dated 2018-07-25 and 1.1 dated 2019-02-06
DESCRIPTION | 8 MD5 | 55 ++--- NAMESPACE | 4 NEWS | 4 R/plotp.R |only R/schweder.R | 4 build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 6 inst/doc/compare.R |only inst/doc/compare.Rnw |only inst/doc/compare.pdf |only inst/doc/metap.R | 86 +------- inst/doc/metap.Rnw | 522 ++++---------------------------------------------- inst/doc/metap.pdf |binary man/allmetap.Rd | 2 man/invchisq.Rd | 25 -- man/invt.Rd | 25 +- man/logitp.Rd | 13 - man/macros |only man/meanp.Rd | 13 - man/meanz.Rd | 19 - man/package-data.Rd | 6 man/plotp.Rd |only man/sumlog.Rd | 24 -- man/sump.Rd | 33 +-- man/sumz.Rd | 17 - man/two2one.Rd | 12 - man/votep.Rd | 17 - man/wilkinsonp.Rd | 25 -- vignettes/compare.Rnw |only vignettes/metap.Rnw | 522 ++++---------------------------------------------- 32 files changed, 227 insertions(+), 1215 deletions(-)
Title: Teaching Data for Statistics and Data Science
Description: Provides data sets for teaching statistics and data science courses.
It includes a sample of data from John Edmund Kerrich's famous
coinflip experiment. These are data that I use for teaching SOC 4015 / SOC
5050 at Saint Louis University (SLU). The package also contains an R Markdown
template with the required formatting for assignments in my courses
SOC 4015, SOC 4650, SOC 5050, and SOC 5650 at SLU.
Author: Christopher Prener [aut, cre] (<https://orcid.org/0000-0002-4310-9888>)
Maintainer: Christopher Prener <chris.prener@slu.edu>
Diff between testDriveR versions 0.4.0 dated 2018-08-31 and 0.5.1 dated 2019-02-06
DESCRIPTION | 20 +++++++++++--------- MD5 | 13 ++++++++----- NEWS.md | 8 ++++++++ R/auto17.R | 2 +- README.md | 26 ++++++++++++++++++++++++-- inst/rmarkdown |only man/auto17.Rd | 2 +- man/figures/template.png |only 8 files changed, 53 insertions(+), 18 deletions(-)
Title: Serializable Representations
Description: String and binary representations of objects for several formats /
mime types.
Author: Philipp Angerer [aut, cre] (<https://orcid.org/0000-0002-0369-2888>),
Thomas Kluyver [aut],
Jan Schulz [aut],
abielr [ctb],
Denilson Figueiredo de Sa [ctb],
Jim Hester [ctb],
karldw [ctb],
Dave Foster [ctb],
Carson Sievert [ctb]
Maintainer: Philipp Angerer <phil.angerer@gmail.com>
Diff between repr versions 0.19.1 dated 2019-01-02 and 0.19.2 dated 2019-02-06
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/utils.r | 3 ++- tests/testthat/test_array_manipulation.r | 2 ++ tests/testthat/test_repr_list.r | 12 ++++++++++++ 5 files changed, 23 insertions(+), 8 deletions(-)
Title: Manipulate and Play 'ProTracker' Modules
Description: 'ProTracker' is a popular music tracker to sequence
music on a Commodore Amiga machine. This package offers the
opportunity to import, export, manipulate and play 'ProTracker'
module files. Even though the file format could be considered
archaic, it still remains popular to this date. This package
intends to contribute to this popularity and therewith
keeping the legacy of 'ProTracker' and the Commodore Amiga
alive.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between ProTrackR versions 0.3.5 dated 2017-10-14 and 0.3.6 dated 2019-02-06
DESCRIPTION | 9 +-- MD5 | 91 ++++++++++++++++--------------- NAMESPACE | 6 ++ NEWS | 36 ++++++++++++ R/02PTCell.r | 13 +++- R/03PTTrack.r | 4 - R/05PTSample.r | 135 ++++++++++------------------------------------ R/06PTModule.r | 88 ++++++++++++++++++++++++----- R/08coercion.r | 4 - R/09playing_routines.r | 108 +++++++++++++++++++++++++++--------- R/10ModArchiveHelpers.r | 6 +- R/11MODPlugHelpers.r | 6 +- R/12ModLandHelpers.r |only R/ProTrackR.r | 4 - man/MODPlugToPTPattern.Rd | 4 - man/PTModule-class.Rd | 5 + man/PTTrack-class.Rd | 4 - man/appendPattern.Rd | 5 + man/as.raw.Rd | 20 +++++- man/clearSamples.Rd | 5 + man/clearSong.Rd | 5 + man/deletePattern.Rd | 5 + man/fix.PTModule.Rd | 5 + man/loopSample.Rd | 2 man/modArchive.Rd | 7 +- man/modLand.Rd |only man/modToWave.Rd | 16 ++++- man/moduleSize.Rd | 5 + man/nybble.Rd | 2 man/nybbleToSignedInt.Rd | 1 man/patternLength.Rd | 5 + man/patternOrder.Rd | 5 + man/patternOrderLength.Rd | 5 + man/playMod.Rd | 4 - man/playWave.Rd | 15 ++++- man/playingtable.Rd | 4 - man/rawToCharNull.Rd | 1 man/rawToPTModule.Rd |only man/rawToSignedInt.Rd | 2 man/rawToUnsignedInt.Rd | 2 man/read.module.Rd | 4 - man/read.sample.Rd | 6 +- man/signedIntToNybble.Rd | 2 man/signedIntToRaw.Rd | 2 man/trackerFlag.Rd | 4 - man/unsignedIntToRaw.Rd | 2 man/write.module.Rd | 4 - man/write.sample.Rd | 3 - 48 files changed, 406 insertions(+), 265 deletions(-)
Title: Measuring Multivariate Dependence Using Distance Multivariance
Description: Distance multivariance is a measure of dependence which can be used to detect
and quantify dependence. The necessary functions are implemented in this packages,
and examples are given. For the theoretic background we refer to the papers:
B. Böttcher, M. Keller-Ressel, R.L. Schilling, Detecting independence of random vectors: generalized distance covariance and Gaussian covariance. VMSTA, 2018, Vol. 5, No. 3, 353-383. <arXiv:1711.07778>.
B. Böttcher, M. Keller-Ressel, R.L. Schilling, Distance multivariance: New dependence measures for random vectors. <arXiv:1711.07775>.
B. Böttcher, Dependence and Dependence Structures: Estimation and Visualization Using Distance Multivariance. <arXiv:1712.06532>.
G. Berschneider, B. Böttcher, On complex Gaussian random fields, Gaussian quadratic forms and sample distance multivariance. <arXiv:1808.07280>.
Author: Björn Böttcher [aut, cre],
Martin Keller-Ressel [ctb]
Maintainer: Björn Böttcher <bjoern.boettcher@tu-dresden.de>
Diff between multivariance versions 1.2.1 dated 2019-01-04 and 2.0.0 dated 2019-02-06
multivariance-1.2.1/multivariance/man/cdm.product.Rd |only multivariance-2.0.0/multivariance/DESCRIPTION | 12 multivariance-2.0.0/multivariance/MD5 | 68 multivariance-2.0.0/multivariance/NAMESPACE | 3 multivariance-2.0.0/multivariance/R/RcppExports.R | 20 multivariance-2.0.0/multivariance/R/multivariance-functions.R | 860 +++++++--- multivariance-2.0.0/multivariance/inst/NEWS | 27 multivariance-2.0.0/multivariance/inst/examples/dependence-structures.R | 4 multivariance-2.0.0/multivariance/man/cdm.Rd | 9 multivariance-2.0.0/multivariance/man/cdm.mu.bcd.Rd | 4 multivariance-2.0.0/multivariance/man/cdms.Rd | 2 multivariance-2.0.0/multivariance/man/cdms.mu.bcd.Rd | 2 multivariance-2.0.0/multivariance/man/clean.graph.Rd | 2 multivariance-2.0.0/multivariance/man/d2.Rd | 4 multivariance-2.0.0/multivariance/man/dependence.structure.Rd | 8 multivariance-2.0.0/multivariance/man/dist.to.matrix.Rd | 2 multivariance-2.0.0/multivariance/man/double.center.Rd |only multivariance-2.0.0/multivariance/man/doubleCenterSymMat.Rd |only multivariance-2.0.0/multivariance/man/fastEuclideanCdm.Rd |only multivariance-2.0.0/multivariance/man/fastdist.Rd | 2 multivariance-2.0.0/multivariance/man/find.cluster.Rd | 6 multivariance-2.0.0/multivariance/man/independence.test.Rd | 8 multivariance-2.0.0/multivariance/man/m.multivariance.Rd | 6 multivariance-2.0.0/multivariance/man/multicorrelation.Rd | 34 multivariance-2.0.0/multivariance/man/multivariance-package.Rd | 12 multivariance-2.0.0/multivariance/man/multivariance.Rd | 24 multivariance-2.0.0/multivariance/man/multivariance.test.Rd |only multivariance-2.0.0/multivariance/man/multivariance.timing.Rd |only multivariance-2.0.0/multivariance/man/multivariances.all.Rd | 8 multivariance-2.0.0/multivariance/man/pearson.pvalue.Rd | 13 multivariance-2.0.0/multivariance/man/pearson.qf.Rd | 2 multivariance-2.0.0/multivariance/man/resample.multivariance.Rd | 2 multivariance-2.0.0/multivariance/man/resample.pvalue.Rd | 4 multivariance-2.0.0/multivariance/man/sample.cdms.Rd | 12 multivariance-2.0.0/multivariance/man/total.multivariance.Rd | 4 multivariance-2.0.0/multivariance/src/RcppExports.cpp | 26 multivariance-2.0.0/multivariance/src/multivariance.cpp | 102 + multivariance-2.0.0/multivariance/tests/testthat/testmultivariances.R | 143 + 38 files changed, 1109 insertions(+), 326 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package 'pan', 'jomo' is a package for multilevel joint modelling multiple imputation (Carpenter and Kenward, 2013) <doi: 10.1002/9781119942283>.
Novel aspects of 'jomo' are the possibility of handling binary and categorical data through latent normal variables, the option to use cluster-specific covariance matrices and to impute compatibly with the substantive model.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <m.quartagno@ucl.ac.uk>
Diff between jomo versions 2.6-6 dated 2019-01-22 and 2.6-7 dated 2019-02-06
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/jomo.clmm.MCMCchain.R | 2 +- R/jomo.clmm.R | 2 +- R/jomo.glm.MCMCchain.R | 4 ++-- R/jomo.glm.R | 4 ++-- R/jomo.glmer.MCMCchain.R | 4 ++-- R/jomo.glmer.R | 4 ++-- R/jomo.polr.MCMCchain.R | 2 +- R/jomo.polr.R | 2 +- src/jomo1glmerbinC.c | 2 -- 11 files changed, 26 insertions(+), 28 deletions(-)
Title: Collection of Tools for Genomic Data Analysis
Description: A loose collection of tools for the analysis of expression and genotype data, currently with the main focus on (e)QTL and MDR analysis.
Author: Daniel Fischer
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>
Diff between GenomicTools versions 0.2.6 dated 2017-07-11 and 0.2.8 dated 2019-02-06
GenomicTools-0.2.6/GenomicTools/R/importGFF3.R |only GenomicTools-0.2.6/GenomicTools/R/importGTF.R |only GenomicTools-0.2.6/GenomicTools/R/importPED.R |only GenomicTools-0.2.6/GenomicTools/R/importSTARLog.R |only GenomicTools-0.2.6/GenomicTools/R/importVCF.R |only GenomicTools-0.2.6/GenomicTools/man/importGFF3.Rd |only GenomicTools-0.2.6/GenomicTools/man/importGTF.Rd |only GenomicTools-0.2.6/GenomicTools/man/importPED.Rd |only GenomicTools-0.2.6/GenomicTools/man/importSTARLog.Rd |only GenomicTools-0.2.6/GenomicTools/man/importVCF.Rd |only GenomicTools-0.2.8/GenomicTools/DESCRIPTION | 10 - GenomicTools-0.2.8/GenomicTools/MD5 | 75 ++++------ GenomicTools-0.2.8/GenomicTools/NAMESPACE | 8 - GenomicTools-0.2.8/GenomicTools/R/QTL.R | 60 ++++++-- GenomicTools-0.2.8/GenomicTools/R/aaa.R | 14 + GenomicTools-0.2.8/GenomicTools/R/diverseFunctions.R |only GenomicTools-0.2.8/GenomicTools/R/eqtl.R | 64 ++++++-- GenomicTools-0.2.8/GenomicTools/R/eqtlDir.R | 11 + GenomicTools-0.2.8/GenomicTools/R/eqtlLM.R | 16 +- GenomicTools-0.2.8/GenomicTools/R/genotypePlot.R | 10 - GenomicTools-0.2.8/GenomicTools/R/getRSLocation.R | 15 +- GenomicTools-0.2.8/GenomicTools/R/gtfToBed.R | 8 - GenomicTools-0.2.8/GenomicTools/R/joinEQTL.R | 5 GenomicTools-0.2.8/GenomicTools/R/plot.eqtl.trans.R | 7 GenomicTools-0.2.8/GenomicTools/R/plot.qtlRes.R | 7 GenomicTools-0.2.8/GenomicTools/R/print.PedMap.R | 5 GenomicTools-0.2.8/GenomicTools/R/print.eqtl.R | 7 GenomicTools-0.2.8/GenomicTools/R/print.qtlRes.R | 28 ++- GenomicTools-0.2.8/GenomicTools/R/print.vcf.R | 2 GenomicTools-0.2.8/GenomicTools/R/rearrange.R | 4 GenomicTools-0.2.8/GenomicTools/R/summary.PedMap.R | 4 GenomicTools-0.2.8/GenomicTools/R/summary.eqtl.R | 34 +++- GenomicTools-0.2.8/GenomicTools/build/vignette.rds |binary GenomicTools-0.2.8/GenomicTools/data/annotTrack.rda |binary GenomicTools-0.2.8/GenomicTools/data/geneEXP.rda |binary GenomicTools-0.2.8/GenomicTools/data/genotData.rda |binary GenomicTools-0.2.8/GenomicTools/data/mdrExample.rda |binary GenomicTools-0.2.8/GenomicTools/data/phenoData.rda |binary GenomicTools-0.2.8/GenomicTools/inst/ChangeLog | 32 ++++ GenomicTools-0.2.8/GenomicTools/inst/doc/GenomicTools-Vignette.pdf |binary GenomicTools-0.2.8/GenomicTools/man/GenomicTools-package.Rd | 4 GenomicTools-0.2.8/GenomicTools/man/QTL.Rd | 2 GenomicTools-0.2.8/GenomicTools/man/getRSLocation.Rd | 11 + GenomicTools-0.2.8/GenomicTools/man/summary.eqtl.Rd | 3 44 files changed, 311 insertions(+), 135 deletions(-)
Title: Post Vortex Simulation Analysis
Description: Facilitate Post Vortex Simulation Analysis by offering
tools to collate multiple Vortex (v10) output files into one R object, and
analyse the collated output statistically. Vortex is a software for
the development of individual-based model for population dynamic simulation
(see <http://www.vortex10.org/Vortex10.aspx>).
Author: Carlo Pacioni [aut, cre],
Florian W. Mayer [aut]
Maintainer: Carlo Pacioni <C.Pacioni@Murdoch.edu.au>
Diff between vortexR versions 1.1.5 dated 2018-05-14 and 1.1.6 dated 2019-02-06
DESCRIPTION | 12 MD5 | 24 - build/vignette.rds |binary data/pac.clas.pairw.rda |binary inst/doc/vortexRguide.html | 626 ++++++++++++++++++++++++++++++--------------- man/Nadults.Rd | 6 man/SSMD_matrix.Rd | 4 man/collate_run.Rd | 4 man/conv_l_yr.Rd | 5 man/fit_regression.Rd | 13 man/line_plot_year_mid.Rd | 4 man/lookup_table.Rd | 4 man/pairwise.Rd | 7 13 files changed, 467 insertions(+), 242 deletions(-)
Title: Principal Components Lasso
Description: A method for fitting the entire regularization path
of the principal components lasso for linear and
logistic regression models. The algorithm uses cyclic coordinate descent
in a path-wise fashion. See URL below for more information on the algorithm.
See Tay, K., Friedman, J. ,Tibshirani, R., (2014) 'Principal component-guided sparse regression'
<arXiv:1810.04651>.
Author: Jerome Friedman, Kenneth Tay, Robert Tibshirani
Maintainer: Rob Tibshirani <tibs@stanford.edu>
Diff between pcLasso versions 1.0 dated 2019-01-11 and 1.1 dated 2019-02-06
DESCRIPTION | 6 MD5 | 19 - NAMESPACE | 1 R/pcLasso.R | 38 ++ R/predict.pcLasso.R | 5 README.md |only inst/doc/pcLasso.html | 584 +++++++++++++++++++++++++++++----------------- man/cv.pcLasso.Rd | 2 man/pcLasso.Rd | 8 man/predict.cv.pcLasso.Rd | 6 man/predict.pcLasso.Rd | 4 11 files changed, 430 insertions(+), 243 deletions(-)
Title: Rolling Statistics
Description: Fast and efficient computation of rolling statistics for time-series data.
Author: Jason Foster
Maintainer: Jason Foster <jason.j.foster@gmail.com>
Diff between roll versions 1.1.1 dated 2018-08-11 and 1.1.2 dated 2019-02-06
DESCRIPTION | 10 MD5 | 25 - NAMESPACE | 2 NEWS.md | 7 R/RcppExports.R | 20 R/roll.R | 190 ++++++++ build/partial.rdb |binary man/roll_all.Rd |only man/roll_any.Rd |only man/roll_max.Rd |only man/roll_median.Rd |only man/roll_min.Rd |only src/RcppExports.cpp | 83 +++ src/init.c | 34 - src/roll.cpp | 376 ++++++++++++++++ src/roll.h | 1183 +++++++++++++++++++++++++++++++++++++++++++++------- 16 files changed, 1742 insertions(+), 188 deletions(-)
Title: Ordinal Forests: Prediction and Variable Ranking with Ordinal
Target Variables
Description: The ordinal forest (OF) method allows ordinal regression with high-dimensional
and low-dimensional data. After having constructed an OF prediction rule using a training dataset,
it can be used to predict the values of the ordinal target variable for new observations.
Moreover, by means of the (permutation-based) variable importance measure of OF, it is also
possible to rank the covariates with respect to their importances in the prediction of the
values of the ordinal target variable.
OF is presented in Hornung (2019).
The main functions of the package are: ordfor() (construction of OF) and predict.ordfor()
(prediction of the target variable values of new observations).
References:
Hornung R. (2019) Ordinal Forests. Journal of Classification,
<doi:10.1007/s00357-018-9302-x>.
Author: Roman Hornung
Maintainer: Roman Hornung <hornung@ibe.med.uni-muenchen.de>
Diff between ordinalForest versions 2.3 dated 2019-01-24 and 2.3-1 dated 2019-02-06
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/ordfor.R | 4 +++- R/predict.ordfor.R | 1 + build/partial.rdb |binary 5 files changed, 12 insertions(+), 9 deletions(-)
Title: Evolutionary Transcriptomics
Description: Investigate the evolution of biological processes by capturing evolutionary signatures in transcriptomes (Drost et al. (2017) <doi:10.1093/bioinformatics/btx835>). The aim of this tool is to provide a transcriptome analysis environment for answering questions regarding the evolution of biological processes (Drost et al. (2016) <doi:10.1101/051565>).
Author: Hajk-Georg Drost [aut, cre] (<https://orcid.org/0000-0002-1567-306X>>>)
Maintainer: Hajk-Georg Drost <hgd23@cam.ac.uk>
Diff between myTAI versions 0.8.0 dated 2018-05-23 and 0.9.0 dated 2019-02-06
myTAI-0.8.0/myTAI/src/registerDynamicSymbol.c |only myTAI-0.9.0/myTAI/DESCRIPTION | 16 myTAI-0.9.0/myTAI/MD5 | 119 ++-- myTAI-0.9.0/myTAI/NAMESPACE | 2 myTAI-0.9.0/myTAI/NEWS.md | 16 myTAI-0.9.0/myTAI/R/DiffGenes.R | 15 myTAI-0.9.0/myTAI/R/EarlyConservationTest.R | 4 myTAI-0.9.0/myTAI/R/FlatLineTest.R | 2 myTAI-0.9.0/myTAI/R/MatchMap.R | 2 myTAI-0.9.0/myTAI/R/PlotCIRatio.R | 2 myTAI-0.9.0/myTAI/R/PlotPattern.R | 2 myTAI-0.9.0/myTAI/R/PlotSignature.R | 112 +++ myTAI-0.9.0/myTAI/R/ReductiveHourglassTest.R | 5 myTAI-0.9.0/myTAI/R/ReverseHourglassTest.R |only myTAI-0.9.0/myTAI/R/TAI.R | 2 myTAI-0.9.0/myTAI/R/TDI.R | 2 myTAI-0.9.0/myTAI/R/bootMatrix.R | 2 myTAI-0.9.0/myTAI/R/combinatorialSignificance.R | 4 myTAI-0.9.0/myTAI/R/reversehourglassScore.R |only myTAI-0.9.0/myTAI/R/rhScore.R | 24 myTAI-0.9.0/myTAI/R/tf.R | 2 myTAI-0.9.0/myTAI/README.md | 20 myTAI-0.9.0/myTAI/build/vignette.rds |binary myTAI-0.9.0/myTAI/inst/doc/Advanced.html | 28 myTAI-0.9.0/myTAI/inst/doc/Enrichment.html | 28 myTAI-0.9.0/myTAI/inst/doc/Expression.html | 28 myTAI-0.9.0/myTAI/inst/doc/Intermediate.R | 33 + myTAI-0.9.0/myTAI/inst/doc/Intermediate.Rmd | 142 ++++ myTAI-0.9.0/myTAI/inst/doc/Intermediate.html | 156 ++++- myTAI-0.9.0/myTAI/inst/doc/Introduction.R | 20 myTAI-0.9.0/myTAI/inst/doc/Introduction.Rmd | 119 +++- myTAI-0.9.0/myTAI/inst/doc/Introduction.html | 110 +++ myTAI-0.9.0/myTAI/inst/doc/Taxonomy.html | 28 myTAI-0.9.0/myTAI/inst/myTAI.png |only myTAI-0.9.0/myTAI/man/CombinatorialSignificance.Rd | 7 myTAI-0.9.0/myTAI/man/DiffGenes.Rd | 15 myTAI-0.9.0/myTAI/man/EarlyConservationTest.Rd | 11 myTAI-0.9.0/myTAI/man/Expressed.Rd | 4 myTAI-0.9.0/myTAI/man/FlatLineTest.Rd | 2 myTAI-0.9.0/myTAI/man/MatchMap.Rd | 2 myTAI-0.9.0/myTAI/man/PlotCIRatio.Rd | 2 myTAI-0.9.0/myTAI/man/PlotCategoryExpr.Rd | 4 myTAI-0.9.0/myTAI/man/PlotDistribution.Rd | 4 myTAI-0.9.0/myTAI/man/PlotEnrichment.Rd | 6 myTAI-0.9.0/myTAI/man/PlotGeneSet.Rd | 4 myTAI-0.9.0/myTAI/man/PlotMeans.Rd | 5 myTAI-0.9.0/myTAI/man/PlotPattern.Rd | 10 myTAI-0.9.0/myTAI/man/PlotRE.Rd | 7 myTAI-0.9.0/myTAI/man/PlotSignature.Rd | 42 - myTAI-0.9.0/myTAI/man/ReductiveHourglassTest.Rd | 12 myTAI-0.9.0/myTAI/man/ReverseHourglassTest.Rd |only myTAI-0.9.0/myTAI/man/TAI.Rd | 2 myTAI-0.9.0/myTAI/man/TDI.Rd | 2 myTAI-0.9.0/myTAI/man/bootMatrix.Rd | 2 myTAI-0.9.0/myTAI/man/reversehourglassScore.Rd |only myTAI-0.9.0/myTAI/man/rhScore.Rd | 23 myTAI-0.9.0/myTAI/man/tf.Rd | 2 myTAI-0.9.0/myTAI/src/Makevars |only myTAI-0.9.0/myTAI/src/RcppExports.cpp | 17 myTAI-0.9.0/myTAI/src/myTAI_init.c |only myTAI-0.9.0/myTAI/src/rcpp_funcs.cpp | 288 ++++------ myTAI-0.9.0/myTAI/tests/testthat/Rplots.pdf |only myTAI-0.9.0/myTAI/tests/testthat/test-CombinatorialSignificance.R | 4 myTAI-0.9.0/myTAI/vignettes/Intermediate.Rmd | 142 ++++ myTAI-0.9.0/myTAI/vignettes/Introduction.Rmd | 119 +++- 65 files changed, 1334 insertions(+), 449 deletions(-)
Title: Continuous Norming
Description: Conventional methods for producing standard scores in psychometrics or biometrics
are often plagued with "jumps" or "gaps" (i.e., discontinuities) in norm tables and low
confidence for assessing extreme scores. The continuous norming method introduced by A.
Lenhard et al. (2016), <doi:10.1177/1073191116656437>, generates continuous test norm
scores on the basis of the raw data from standardization samples, without requiring
assumptions about the distribution of the raw data: Norm scores are directly established
from raw data by modeling the latter ones as a function of both percentile scores and an
explanatory variable (e.g., age). The method minimizes bias arising from sampling and
measurement error, while handling marked deviations from normality, addressing bottom
or ceiling effects and capturing almost all of the variance in the original norm data
sample.
Author: Wolfgang Lenhard [cre, aut] (<https://orcid.org/0000-0002-8184-6889>),
Alexandra Lenhard [aut],
Sebastian Gary [ctb]
Maintainer: Wolfgang Lenhard <wolfgang.lenhard@uni-wuerzburg.de>
Diff between cNORM versions 1.1.2 dated 2018-12-08 and 1.1.5 dated 2019-02-06
DESCRIPTION | 14 +++++++------- MD5 | 24 ++++++++++++------------ NAMESPACE | 2 +- NEWS.md | 44 ++++++++++++++++++++++++++++++++++++++++++-- R/modelling.R | 32 ++++++++++++++++++++++++-------- R/plot.R | 4 ++-- R/preparation.R | 9 ++++++--- README.md | 10 +++++++--- inst/doc/cNORM-Demo.html | 30 ++++++++++++++++++++++++++---- inst/shiny/server.R | 18 ++++++++++++++++++ inst/shiny/ui.R | 37 ++++++++++++++++++++++++++++++++++++- man/cnorm.cv.Rd | 21 ++++++++++++++++----- man/prepareData.Rd | 6 +++++- 13 files changed, 202 insertions(+), 49 deletions(-)
Title: Species-Habitat Associations
Description: Analyse species-habitat associations in R. Therefore, information about the
location of the species is needed and about the environmental conditions. To test
for significance habitat associations, one of the two components is randomized.
Methods are mainly based on Plotkin et al. (2000) <doi:10.1006/jtbi.2000.2158> and
Harms et al. (2001) <doi:10.1111/j.1365-2745.2001.00615.x>.
Author: Maximillian H.K. Hesselbarth [aut, cre]
(<https://orcid.org/0000-0003-1125-9918>),
Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>)
Maintainer: Maximillian H.K. Hesselbarth <maximilian.hesselbarth@uni-goettingen.de>
Diff between shar versions 0.1 dated 2019-01-27 and 0.2 dated 2019-02-06
DESCRIPTION | 10 MD5 | 88 +-- NAMESPACE | 28 - NEWS.md | 16 R/calculate_energy.R | 232 ++++---- R/data.R | 44 - R/fit_point_process.R | 305 +++++------ R/plot_randomized_pattern.R | 494 +++++++++++------- R/randomize_raster.R | 390 +++++++------- R/reconstruct_marks.R | 422 ++++++++------- R/reconstruct_pattern.R | 591 +++++++++++----------- R/results_habitat_association.R | 60 +- R/translate_raster.R | 184 +++--- build/vignette.rds |binary inst/doc/background.html | 528 +++++++++---------- inst/doc/publication_record.html | 474 ++++++++--------- man/calculate_energy.Rd | 97 +-- man/classify_habitats.Rd | 94 +-- man/create_neighbourhood.Rd | 68 +- man/estimate_pcf_fast.Rd | 84 +-- man/extract_points.Rd | 54 +- man/figures/README-plot_habitat_random-1.png |binary man/figures/README-plot_random_pattern-1.png |binary man/fit_point_process.Rd | 82 +-- man/landscape.Rd | 36 - man/plot_randomized_pattern.Rd | 91 +-- man/randomize_raster.Rd | 100 +-- man/reconstruct_marks.Rd | 131 ++-- man/reconstruct_pattern.Rd | 139 ++--- man/results_habitat_association.Rd | 100 +-- man/species_a.Rd | 28 - man/species_b.Rd | 28 - man/translate_raster.Rd | 80 +- tests/testthat/test-calculate_energy.R | 72 +- tests/testthat/test-classify_habitats.R | 22 tests/testthat/test-create_neighbourhood.R | 54 +- tests/testthat/test-estimate_pcf_fast.R | 14 tests/testthat/test-extract_points.R | 38 - tests/testthat/test-fit-point_process.R | 171 +++--- tests/testthat/test-plot_randomized_pattern.R | 111 ++-- tests/testthat/test-randomize_raster.R | 136 ++--- tests/testthat/test-reconstruct_marks.R | 235 ++++---- tests/testthat/test-reconstruct_pattern.R | 179 +++--- tests/testthat/test-results_habitat_association.R | 145 ++--- tests/testthat/test-translate_raster.R | 85 +-- 45 files changed, 3337 insertions(+), 3003 deletions(-)
Title: Test Overlapping of Polygons Against Random Rotation
Description: Tests the observed overlapping polygon area in a collection of polygons against a null model of random rotation, as explained in De la Cruz et al. (2017) <doi:10.13140/RG.2.2.12825.72801>.
Author: Marcelino de la Cruz Rot
Maintainer: Marcelino de la Cruz <marcelino.delacruz@urjc.es>
Diff between overlapptest versions 1.0 dated 2018-05-30 and 1.1 dated 2019-02-06
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/pval.R | 41 +++++++++++++++++++++++++---------------- man/pval.Rd | 7 ++++--- man/rotawin.Rd | 2 +- man/test.intersection.Rd | 11 +++++------ 6 files changed, 44 insertions(+), 35 deletions(-)
Title: File Handlers for Genomic Data Analysis
Description: A collection of I/O tools for handling the most commonly used genomic datafiles, like fasta/-q, bed, gff, gtf, ped/map and vcf.
Author: Daniel Fischer
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>
Diff between GenomicTools.fileHandler versions 0.1.2 dated 2018-08-16 and 0.1.4 dated 2019-02-06
GenomicTools.fileHandler-0.1.2/GenomicTools.fileHandler/inst/doc/GenomicTools.fileHandler-Vignette.html |only GenomicTools.fileHandler-0.1.4/GenomicTools.fileHandler/DESCRIPTION | 10 +-- GenomicTools.fileHandler-0.1.4/GenomicTools.fileHandler/MD5 | 25 +++---- GenomicTools.fileHandler-0.1.4/GenomicTools.fileHandler/NAMESPACE | 1 GenomicTools.fileHandler-0.1.4/GenomicTools.fileHandler/R/GenomicTools.fileHandler.R | 2 GenomicTools.fileHandler-0.1.4/GenomicTools.fileHandler/R/S3print.R | 6 + GenomicTools.fileHandler-0.1.4/GenomicTools.fileHandler/R/S3summary.R | 20 ++++++ GenomicTools.fileHandler-0.1.4/GenomicTools.fileHandler/R/importVCF.R | 33 +++++++--- GenomicTools.fileHandler-0.1.4/GenomicTools.fileHandler/build/vignette.rds |binary GenomicTools.fileHandler-0.1.4/GenomicTools.fileHandler/inst/ChangeLog | 6 + GenomicTools.fileHandler-0.1.4/GenomicTools.fileHandler/inst/doc/GenomicTools.fileHandler-Vignette.pdf |only GenomicTools.fileHandler-0.1.4/GenomicTools.fileHandler/man/GenomicTools.fileHandler-package.Rd | 2 GenomicTools.fileHandler-0.1.4/GenomicTools.fileHandler/man/importVCF.Rd | 3 GenomicTools.fileHandler-0.1.4/GenomicTools.fileHandler/man/print.fq.Rd | 4 - GenomicTools.fileHandler-0.1.4/GenomicTools.fileHandler/man/summary.gtf.Rd |only 15 files changed, 81 insertions(+), 31 deletions(-)
More information about GenomicTools.fileHandler at CRAN
Permanent link
Title: Generalized Mortality Estimator
Description: Command-line and 'shiny' GUI implementation of the GenEst models for estimating bird and bat mortality at wind and solar power facilities, following Dalthorp, et al. (2018) <doi:10.3133/tm7A2>.
Author: Daniel Dalthorp [aut, cre],
Juniper Simonis [aut],
Lisa Madsen [aut],
Manuela Huso [aut],
Paul Rabie [aut],
Jeffrey Mintz [aut],
Robert Wolpert [aut],
Jared Studyvin [aut],
Franzi Korner-Nievergelt [aut]
Maintainer: Daniel Dalthorp <ddalthorp@usgs.gov>
Diff between GenEst versions 1.2.1 dated 2018-12-19 and 1.2.2 dated 2019-02-06
DESCRIPTION | 8 - MD5 | 24 +-- NAMESPACE | 1 R/app_content.R | 20 +-- R/app_ui.R | 64 +++++++-- R/app_update_rv.R | 6 R/detection_probability_functions.R | 3 R/mortality_functions.R | 4 build/vignette.rds |binary inst/doc/GenEstGUI.html | 4 inst/doc/command-line-example.html | 142 ++++++++++++--------- inst/doc/solar-examples.html | 54 +++++--- inst/doc/wind-examples.html | 240 +++++++++++++++++++----------------- 13 files changed, 337 insertions(+), 233 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a (bio)marker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's Seventh Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Paul Meyvisch, Alvaro Florez Poveda, Ariel Alonso, Hannah M. Ensor, Christopher J. Weir & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between Surrogate versions 1.1 dated 2018-10-18 and 1.2 dated 2019-02-06
Surrogate-1.1/Surrogate/data/CIGTS.rda |only Surrogate-1.1/Surrogate/data/CIGTS_BinCont.rda |only Surrogate-1.1/Surrogate/man/CIGTS.Rd |only Surrogate-1.1/Surrogate/man/CIGTS_BinCont.Rd |only Surrogate-1.2/Surrogate/DESCRIPTION | 6 +++--- Surrogate-1.2/Surrogate/MD5 | 6 +----- 6 files changed, 4 insertions(+), 8 deletions(-)