Title: Efficient Estimation of Discrete-Time Multivariate Frailty Model
Using Exact Likelihood Function for Grouped Survival Data
Description: The core of this 'Rcpp' based package is several functions to estimate the baseline hazard, frailty variance, and fixed effect parameter for a discrete-time shared frailty model with random effects. The functions are designed to analyze grouped time-to-event data accounting for family structure of related individuals (i.e., trios). The core functions include two processes: (1) evaluate the multivariable integration to compute the exact proportional hazards model based likelihood and (2) estimate the desired parameters using maximum likelihood estimation. The integration is evaluated by the 'Cuhre' algorithm from the 'Cuba' library (Hahn, T., Cuba-a library for multidimensional numerical integration, Comput. Phys. Commun. 168, 2005, 78-95 <doi:10.1016/j.cpc.2005.01.010>), and the source files of the 'Cuhre' function are included in this package. The maximization process is carried out using Brent's algorithm, with the 'C++' code file from John Burkardt and John Denker (Brent, R.,Algorithms for Minimization without Derivatives, Dover, 2002, ISBN 0-486-41998-3).
Author: Jiaxing Lin, Alexander Sibley, Tracy Truong, Nancy Cox, Eileen Dolan, Yu
Jiang, Janice McCarthy, Andrew Allen, Kouros Owzar, Zhiguo Li
Maintainer: Jiaxing Lin <jiaxing.lin@duke.edu>
Diff between lclGWAS versions 1.0.1 dated 2016-11-15 and 1.0.2 dated 2016-11-30
DESCRIPTION | 23 ++------ MD5 | 38 +++++++------- NEWS | 9 +++ R/RcppExports.R | 12 ++-- inst/doc/lclGWAS.R | 56 +++++++++------------ inst/doc/lclGWAS.Rnw | 128 ++++++++++++++++++++++++------------------------- inst/doc/lclGWAS.pdf |binary man/alphaEst.Rd | 19 +++---- man/betaEst.Rd | 32 +++++------- man/lclGWAS-package.Rd | 12 ++-- man/varEst.Rd | 30 +++++------ src/RcppExports.cpp | 26 ++++----- src/alphaEst.cpp | 41 ++++++--------- src/betaEst.cpp | 25 +++++---- src/famSize.h |only src/fam_LLBeta.h | 12 +++- src/fam_LLVar.h | 9 ++- src/integrand.h | 21 +++----- src/likelihood_ind.h |only src/varEst.cpp | 21 ++++---- vignettes/lclGWAS.Rnw | 128 ++++++++++++++++++++++++------------------------- 21 files changed, 317 insertions(+), 325 deletions(-)
Title: Classes and Methods for Seismic Data Analysis
Description: Provides classes and methods for seismic data analysis. The
base classes and methods are inspired by the python code found in
the 'ObsPy' python toolbox <https://github.com/obsypy/obspy>. Additional classes and
methods support data returned by web services provided by the 'IRIS DMC'
<http://service.iris.edu/>.
Author: Jonathan Callahan [aut],
Rob Casey [aut],
Gillian Sharer [aut, cre],
Mary Templeton [aut]
Maintainer: Gillian Sharer <gillian@iris.washington.edu>
Diff between IRISSeismic versions 1.0.7-1 dated 2016-04-20 and 1.3.8 dated 2016-11-30
DESCRIPTION | 25 MD5 | 135 +- NAMESPACE | 4 R/Class-IrisClient.R | 666 ++++++++---- R/Class-Stream.R | 125 +- R/Class-Trace.R | 83 + R/Utils.R | 132 +- R/spectralUtils.R | 170 ++- build/vignette.rds |binary inst/doc/IRISSeismic-intro.R | 16 inst/doc/IRISSeismic-intro.Rnw | 9 inst/doc/IRISSeismic-intro.pdf |binary man/DDT.Rd | 4 man/IRISSeismic-package.Rd | 128 ++ man/IrisClient-class.Rd | 8 man/McNamaraBins.Rd | 2 man/McNamaraPSD.Rd | 2 man/STALTA.Rd | 4 man/Stream-class.Rd | 8 man/Trace-class.Rd | 16 man/TraceHeader-class.Rd | 20 man/basicStats.Rd | 6 man/butterworth.Rd | 8 man/crossSpectrum.Rd | 12 man/envelope.Rd | 2 man/eventWindow.Rd | 2 man/getAvailability.Rd | 13 man/getChannel.Rd | 15 man/getDataselect.Rd | 49 man/getDistaz.Rd | 13 man/getEvalresp.Rd | 2 man/getEvent.Rd | 8 man/getGaps.Rd | 8 man/getNetwork.Rd | 14 man/getRotation.Rd | 2 man/getSNCL.Rd | 35 man/getStation.Rd | 15 man/getTraveltime.Rd | 4 man/getUnavailability.Rd | 18 man/getUpDownTimes.Rd | 7 man/hilbert.Rd | 5 man/hilbertFFT.Rd | 2 man/mergeTraces.Rd | 2 man/mergeUpDownTimes.Rd | 2 man/miniseed2Stream.Rd | 16 man/multiplyBy.Rd | 23 man/noiseMatrix2PdfMatrix.Rd | 2 man/noiseModels.Rd | 6 man/psdDF2NoiseMatrix.Rd | 10 man/psdList.Rd | 8 man/psdList2NoiseMatrix.Rd | 12 man/psdPlot.Rd | 9 man/psdStatistics.Rd | 13 man/readMiniseedFile.Rd | 16 man/rmsVariance.Rd | 6 man/rotate2D.Rd | 24 man/slice.Rd | 2 man/surfaceDistance.Rd | 2 man/triggerOnset.Rd | 4 man/unHistogram.Rd |only src/Makevars.win | 4 src/libmseed/Makefile | 4 src/libmseed/fileutils.c | 2 src/libmseed/genutils.c | 2 src/libmseed/libmseed.h | 14 src/libmseed/tracelist.c | 2213 ++++++++++++++++++++-------------------- src/libmseed/unpackdata.c | 13 src/parseMiniSEED.c | 77 - vignettes/IRISSeismic-intro.Rnw | 9 69 files changed, 2543 insertions(+), 1749 deletions(-)
Title: Exploratory Data Analysis using Random Forests
Description: Functions useful for exploratory data analysis
using random forests which can be used to compute multivariate partial
dependence, observation, class, and variable-wise marginal and joint permutation
importance as well as observation-specific measures of distance
(supervised or unsupervised). All of the aforementioned functions are
accompanied by 'ggplot2' plotting functions.
Author: Zachary M. Jones <zmj@zmjones.com> and Fridolin Linder
<fridolin.linder@gmail.com>
Maintainer: Zachary M. Jones <zmj@zmjones.com>
Diff between edarf versions 1.0.0 dated 2016-10-24 and 1.1.0 dated 2016-11-30
DESCRIPTION | 12 - MD5 | 45 ++--- NAMESPACE | 16 -- R/imp.R | 235 +++++++++++++++--------------- R/pd.R | 349 +++++++++++++++++++++------------------------ R/plot.R | 227 ++++++++--------------------- R/prox.R | 22 ++ R/utils.R |only README.md | 5 build/vignette.rds |binary inst/doc/edarf.R | 38 +--- inst/doc/edarf.Rmd | 62 ++----- inst/doc/edarf.html | 107 ++++++------- man/extract_proximity.Rd | 4 man/partial_dependence.Rd | 40 ++--- man/plot_imp.Rd | 29 --- man/plot_pd.Rd | 7 man/plot_pred.Rd | 6 man/variable_importance.Rd | 29 +-- tests/testthat.R | 9 - tests/testthat/test_imp.R | 53 +----- tests/testthat/test_pd.R | 50 +++--- tests/testthat/test_prox.R | 6 vignettes/edarf.Rmd | 62 ++----- 24 files changed, 605 insertions(+), 808 deletions(-)
Title: Multivariate Normality Tests
Description: Performs multivariate normality tests and graphical approaches and implements multivariate outlier detection and univariate normality of marginal distributions through plots and tests.
Author: Selcuk Korkmaz [aut, cre], Dincer Goksuluk [aut], Gokmen Zararsiz [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between MVN versions 4.0 dated 2015-06-03 and 4.0.1 dated 2016-11-30
DESCRIPTION | 16 ++++++------ MD5 | 34 ++++++++++++++------------ NAMESPACE | 38 ++++++++++++++--------------- R/contourControl.R |only R/hzTest.R | 1 R/mardiaTest.R | 1 R/mvnPlot.R | 64 ++++++++++++++++++++++++++++++-------------------- R/perspControl.R |only R/roystonTest.R | 1 build/vignette.rds |binary inst/CITATION | 2 - inst/doc/MVN.Rnw | 4 +-- inst/doc/MVN.pdf |binary man/contourControl.Rd |only man/hzTest.Rd | 4 +++ man/mardiaTest.Rd | 4 +++ man/mvnPlot.Rd | 8 +++++- man/perspControl.Rd |only man/roystonTest.Rd | 4 +++ vignettes/MVN.Rnw | 4 +-- 20 files changed, 111 insertions(+), 74 deletions(-)
Title: Quantitative Analysis of Motion
Description: Statistics to quantify tracks of moving things (x-y-z-t data),
such as cells, bacteria or animals. Available measures include mean square
displacement, confinement ratio, autocorrelation, straightness, turning angle,
and fractal dimension.
Author: Johannes Textor, Katharina Dannenberg, Jeffrey Berry, Gerhard Burger
Maintainer: Johannes Textor <johannes.textor@gmx.de>
Diff between MotilityLab versions 0.2-4 dated 2015-11-19 and 0.2-5 dated 2016-11-30
DESCRIPTION | 10 MD5 | 21 NAMESPACE | 3 R/functions.R | 2475 +++++++++++++-------------- R/internal.R | 350 +-- R/simulate-tracks.R | 360 +-- R/track-measures.R | 544 ++--- R/track-set-transformations.R | 230 +- man/as.tracks.data.frame.Rd |only man/read.tracks.csv.Rd | 6 tests/testthat/ref_tracks.RData |only tests/testthat/ref_tracks.csv |only tests/testthat/ref_tracks_blank_line_sep.csv |only tests/testthat/testLoadingTracks.R |only 14 files changed, 2016 insertions(+), 1983 deletions(-)
Title: Categorical Scatter (Violin Point) Plots
Description: Provides two methods of plotting categorical scatter plots such
that the arrangement of points within a category reflects the density of
data at that region, and avoids over-plotting.
Author: Erik Clarke [aut, cre],
Scott Sherrill-Mix [aut]
Maintainer: Erik Clarke <erikclarke@gmail.com>
Diff between ggbeeswarm versions 0.5.0 dated 2016-02-21 and 0.5.2 dated 2016-11-30
DESCRIPTION | 11 +++++--- MD5 | 23 ++++++++++------ R/geom-beeswarm.R | 18 ++++++++++--- R/geom-quasirandom.R | 21 ++++++++++++--- R/position-beeswarm.R | 60 ++++++++++++++++++++++++++------------------ R/position-quasirandom.R | 58 ++++++++++++++++++++++++++---------------- build/partial.rdb |binary build/vignette.rds |only inst |only man/geom_beeswarm.Rd | 34 +++++++++++++----------- man/geom_quasirandom.Rd | 38 +++++++++++++++------------ man/position_quasirandom.Rd | 4 +- vignettes |only 13 files changed, 166 insertions(+), 101 deletions(-)
Title: Fitting log-Linear Models in Sparse Contingency Tables
Description: Log-linear modeling is a popular method for the analysis of contingency table data. When the table is sparse, the data can fall on the boundary of the convex support, and we say that "the MLE does not exist" in the sense that some parameters cannot be estimated. However, an extended MLE always exists, and a subset of the original parameters will be estimable. The 'eMLEloglin' package determines which sampling zeros contribute to the non-existence of the MLE. These problematic zero cells can be removed from the contingency table and the model can then be fit (as far as is possible) using the glm() function.
Author: Matthew Friedlander
Maintainer: Matthew Friedlander <mattyf5@hotmail.com>
Diff between eMLEloglin versions 1.0 dated 2016-11-23 and 1.0.1 dated 2016-11-30
eMLEloglin-1.0.1/eMLEloglin/DESCRIPTION | 10 ++++------ eMLEloglin-1.0.1/eMLEloglin/MD5 | 17 ++++++++--------- eMLEloglin-1.0.1/eMLEloglin/build/vignette.rds |binary eMLEloglin-1.0.1/eMLEloglin/inst/doc/User_manual.Rnw |only eMLEloglin-1.0.1/eMLEloglin/inst/doc/User_manual.pdf |binary eMLEloglin-1.0.1/eMLEloglin/man/eMLEloglin.Rd | 10 ++++++---- eMLEloglin-1.0.1/eMLEloglin/man/facial_set.Rd | 6 ++++-- eMLEloglin-1.0.1/eMLEloglin/man/rochdale.Rd | 2 +- eMLEloglin-1.0.1/eMLEloglin/vignettes/User_manual.Rnw |only eMLEloglin-1.0/eMLEloglin/inst/doc/User_manual.ltx |only eMLEloglin-1.0/eMLEloglin/vignettes/User_manual.ltx |only eMLEloglin-1.0/eMLEloglin/vignettes/mybib.bib |only 12 files changed, 23 insertions(+), 22 deletions(-)
Title: Approximate Bayesian Computation via Random Forests
Description: Performs Approximate Bayesian Computation (ABC) model choice and parameter inference via random forests.
Author: Jean-Michel Marin [aut, cre],
Louis Raynal [aut],
Pierre Pudlo [aut],
Christian P. Robert [ctb],
Arnaud Estoup [ctb]
Maintainer: Jean-Michel Marin <jean-michel.marin@umontpellier.fr>
Diff between abcrf versions 1.3 dated 2016-06-03 and 1.4 dated 2016-11-30
DESCRIPTION | 20 +- MD5 | 54 +++---- NAMESPACE | 19 +- R/abcrf.R | 173 +++++++++++----------- R/covRegAbcrf.R | 108 ++++++++------ R/densityPlot.R | 74 ++++++--- R/err.abcrf.R | 81 ++++++---- R/err.regAbcrf.R |only R/plot.abcrf.R | 50 ++++-- R/plot.regAbcrf.R | 11 - R/predict.abcrf.R | 93 ++++++++---- R/predict.regAbcrf.R | 343 +++++++++++++++++++++++---------------------- R/readRefTable.R |only R/regAbcrf.R | 84 ++++++----- R/variableImpPlot.R |only data/datalist | 2 data/snp.obs.RData |binary man/abcrf.Rd | 31 +--- man/covRegAbcrf.Rd | 51 ++++-- man/densityPlot.Rd | 36 ++-- man/err.abcrf.Rd | 12 + man/err.regAbcrf.Rd |only man/plot.abcrf.Rd | 15 + man/plot.regAbcrf.Rd | 31 ++-- man/predict.abcrf.Rd | 22 +- man/predict.regAbcrf.Rd | 36 ++-- man/readRefTable.Rd |only man/regAbcrf.Rd | 47 +++--- man/snp.Rd | 2 man/variableImpPlot.Rd |only src/findweightsAmelioree.c | 39 +---- 31 files changed, 811 insertions(+), 623 deletions(-)
Title: Data Exchange Between R and LabKey Server
Description: The LabKey client library for R makes it easy for R users to
load live data from a LabKey Server, <http://www.labkey.com/>,
into the R environment for analysis, provided users have permissions
to read the data. It also enables R users to insert, update, and
delete records stored on a LabKey Server, provided they have appropriate
permissions to do so.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>
Diff between Rlabkey versions 2.1.131 dated 2016-09-26 and 2.1.132 dated 2016-11-30
DESCRIPTION | 15 ++++++++++----- MD5 | 42 +++++++++++++++++++++--------------------- NEWS | 5 +++++ R/ifcookie.R | 2 +- R/labkey.deleteRows.R | 2 +- R/labkey.getFolders.R | 2 +- R/labkey.getQueryInfo.R | 2 +- R/labkey.getQueryLists.R | 2 +- R/labkey.getSchemas.R | 2 +- R/labkey.importRows.R | 2 +- R/labkey.insertRows.R | 2 +- R/labkey.saveBatch.R | 4 ++-- R/labkey.setCurlOptions.R | 2 +- R/labkey.updateRows.R | 2 +- R/makeDF.R | 17 +++++++++++++---- R/makeFilter.R | 6 ++++++ R/schemaObjects.R | 2 +- build/vignette.rds |binary man/Rlabkey-package.Rd | 6 +++--- man/labkey.getQueries.Rd | 2 +- man/labkey.getSchemas.Rd | 2 +- man/makeFilter.Rd | 3 ++- 22 files changed, 75 insertions(+), 49 deletions(-)
Title: Tools for Grid-Based Survey Sampling Design
Description: Multi-stage cluster household surveys are commonly performed by
governments and programs to monitor population demographic, social,
economic, and health outcomes. In these surveys, communities are sampled
in a first stage of sampling from within subpopulations of interest
(or strata), households are sampled in a second stage of sampling, and
sometimes individuals are listed and further sampled within households.
The first stage of sampling, where communities of sample populations are
defined, are called Primary Sampling Units (PSUs) while the households
are secondary sampling units (SSUs). Census data are typically used to
select PSUs within strata. If census data are outdated, inaccurate, or
not available at fine enough scale, however, gridded population data can
be used instead. This tool selects PSUs within user-defined strata using
gridded population data, given desired numbers of sampled households
within each PSU. The population densities used to create PSUs are drawn
from rasters such as the population data from the WorldPop Project
(http://www.worldpop.org.uk). PSUs are defined within a stratum using a
serpentine sampling method, and can be set to have a certain ratio of
urban and rural PSUs, or to be evenly distributed across a coarse,
user-defined grid.
Author: Dana R. Thomson (University of Southampton), Nick W. Ruktanonchai
(University of Southampton), Forrest R. Stevens (University of Louisville),
Marcia Castro (Harvard University), Andrew J. Tatem (University of Southampton)
Maintainer: Nick Ruktanonchai <nrukt00@gmail.com>
Diff between gridsample versions 0.1.2 dated 2016-11-24 and 0.1.3 dated 2016-11-30
DESCRIPTION | 12 ++++++------ LICENSE |only MD5 | 3 ++- 3 files changed, 8 insertions(+), 7 deletions(-)
Title: Clinical Trial Design and Data Analysis Functions
Description: Utilities to make your clinical collaborations easier if not
fun. It contains functions for designing studies such as Simon
2-stage and group sequential designs and for data analysis such
as Jonckheere-Terpstra test and estimating survival quantiles.
Author: Venkatraman E. Seshan
Maintainer: Venkatraman E. Seshan <seshanv@mskcc.org>
Diff between clinfun versions 1.0.12 dated 2016-10-17 and 1.0.13 dated 2016-11-30
CHANGES | 5 +++++ DESCRIPTION | 11 +++++++---- MD5 | 6 +++--- R/permlogrank.R | 4 ++-- 4 files changed, 17 insertions(+), 9 deletions(-)
Title: eXtraction of ENTity
Description: Provides a tool for extracting information (entities and relations between them) in text datasets. It also emphasizes the results exploration with graphical displays. It is a rule-based system and works with hand-made dictionaries and local grammars defined by users. 'x.ent' uses parsing with Perl functions and JavaScript to define user preferences through a browser and R to display and support analysis of the results extracted. Local grammars are defined and compiled with the tool Unitex, a tool developed by University Paris Est that supports multiple languages. See ?xconfig for an introduction.
Author: Nicolas Turenne [aut],
Tien T. Phan [aut, cre],
John Resig [ctb, cph] (the JavaScript file at
inst/www/jquery-1.11.1.min.js),
Jeroen Ooms [ctb] (the JavaScript file at inst/www/opencpu-0.5.js)
Maintainer: Tien T. Phan <phantien84@gmail.com>
Diff between x.ent versions 1.1.2 dated 2015-03-03 and 1.1.6 dated 2016-11-30
DESCRIPTION | 19 MD5 | 33 NAMESPACE | 5 NEWS | 12 R/config.R | 26 R/parse.R | 11 inst/Perl/CreateCSV.pl |only inst/Perl/CreateSQL.pl |only inst/Perl/Main.pl | 29 inst/Perl/Modules/Entite.pm | 199 ++++ inst/Perl/Modules/Structure.pm | 248 +++--- inst/Perl/Modules/Utils.pm | 28 inst/dico/dico-n_v1.txt |only inst/dico/dico-r_v2.txt | 12 inst/dico/replace.txt | 3 inst/eval/eval.txt | 1658 ++++++++++++++++++++--------------------- inst/www/config.html | 14 man/xconfig.Rd | 6 man/xparse.Rd | 6 19 files changed, 1316 insertions(+), 993 deletions(-)
Title: Fisheries Stock Assessment Simulation Testing with Stock
Synthesis
Description: Develops a framework for fisheries stock assessment simulation
testing with Stock Synthesis 3 (SS3).
Author: Sean Anderson [aut, cre],
Cole Monnahan [aut],
Kelli Johnson [aut],
Kotaro Ono [aut],
Juan Valero [aut],
Curry Cunningham [aut],
Allan Hicks [aut],
Felipe Hurtado-Ferro [aut],
Peter Kuriyama [aut],
Roberto Licandeo [aut],
Carey McGilliard [aut],
Melissa Muradian [ctb],
Merrill Rudd [aut],
Christine Stawitz [aut],
Cody Szuwalski [aut],
Ian Taylor [aut],
Katyana Vert-pre [aut],
Athol Whitten [aut]
Maintainer: Sean Anderson <sean@seananderson.ca>
Diff between ss3sim versions 0.9.2 dated 2016-04-24 and 0.9.3 dated 2016-11-30
DESCRIPTION | 10 - LICENSE | 6 MD5 | 28 +-- NEWS.md | 7 R/get_bin.R | 20 +- README.md | 163 +++++++---------- build/vignette.rds |binary inst/CITATION | 5 inst/doc/introduction.Rmd | 5 inst/doc/introduction.html | 376 +++++++++++++++++++++++------------------ inst/doc/making-functions.html | 19 +- inst/doc/making-models.Rmd | 72 ++++--- inst/doc/making-models.html | 56 +++--- inst/doc/modifying-models.html | 30 ++- vignettes/making-models.Rmd | 72 ++++--- 15 files changed, 468 insertions(+), 401 deletions(-)
Title: Reads Mass Spectrometry Data in Bruker *flex Format
Description: Reads data files acquired by Bruker Daltonics' matrix-assisted
laser desorption/ionization-time-of-flight mass spectrometer of the *flex
series.
Author: Sebastian Gibb [aut, cre]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between readBrukerFlexData versions 1.8.2 dated 2014-12-15 and 1.8.3 dated 2016-11-30
DESCRIPTION | 18 ++++++----- MD5 | 54 +++++++++++++++++------------------ NAMESPACE | 2 - NEWS | 8 +++++ R/double2singlePrecision-functions.R | 7 +--- R/grepAcquValue-functions.R | 24 ++++++--------- R/hpc-functions.R | 29 +++++++----------- R/package.R | 4 +- R/readAcquFile-functions.R | 20 ++++++------ R/readBrukerFlexDir-functions.R | 17 ++++------- R/readBrukerFlexFile-functions.R | 14 +++++++-- R/readFidFile-functions.R | 6 +-- R/sampleName-functions.R | 4 +- man/changePrecision.Rd | 2 - man/cpSpecHpcMzXml.Rd | 6 +-- man/double2singlePrecision.Rd | 5 +-- man/extractHPCConstants.Rd | 6 +-- man/grepAcquDoubleValue.Rd | 2 - man/grepAcquValue.Rd | 2 - man/hpc.Rd | 3 + man/readAcquFile.Rd | 2 - man/readBrukerFlexData-defunct.Rd | 2 - man/readBrukerFlexData-package.Rd | 6 +-- man/readBrukerFlexDir.Rd | 3 + man/readBrukerFlexFile.Rd | 5 +-- man/readFidFile.Rd | 4 +- man/sampleName.Rd | 4 +- man/tof2mass.Rd | 6 +-- 28 files changed, 135 insertions(+), 130 deletions(-)
More information about readBrukerFlexData at CRAN
Permanent link
Title: Robust Model-Based Clustering
Description: Performs robust cluster analysis allowing for outliers and noise that cannot be fitted by any cluster. The data are modelled by a mixture of Gaussian distributions and a noise component, which is an improper uniform distribution covering the whole Euclidean space. Parameters are estimated by (pseudo) maximum likelihood. This is fitted by a EM-type algorithm. See Coretto and Hennig (2015) <https://arxiv.org/abs/1406.0808>, and Coretto and Hennig (2016) <https://arxiv.org/abs/1309.6895>.
Author: Pietro Coretto [aut, cre], Christian Hennig [aut]
Maintainer: Pietro Coretto <pcoretto@unisa.it>
Diff between otrimle versions 0.3 dated 2016-10-05 and 0.4 dated 2016-11-30
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/misc.R | 2 +- R/plotting.R | 40 ++++++++++++++++++++++++++-------------- 4 files changed, 34 insertions(+), 22 deletions(-)
Title: Estimating Conditional Auto-Regressive (CAR) Models using Monte
Carlo Likelihood Methods
Description: The likelihood of direct CAR models and Binomial and Poisson GLM with latent CAR variables are approximated by the Monte Carlo likelihood. The Maximum Monte Carlo likelihood estimator is found either by an iterative procedure of directly maximising the Monte Carlo approximation or by a response surface design method.
Author: Zhe Sha [aut, cre]
Maintainer: Zhe Sha <zhesha1006@gmail.com>
Diff between mclcar versions 0.1.4 dated 2016-08-04 and 0.1-8 dated 2016-11-30
DESCRIPTION | 12 MD5 | 74 - NAMESPACE | 38 R/CAR.simLM.R | 162 +-- R/HCAR.sim.R |only R/OptimMCL.HCAR.R |only R/OptimMCL.R | 406 +++---- R/loglik.dCAR.R | 442 ++++---- R/mcl.HCAR.R |only R/mcl.bin.R | 618 ++++++------ R/mcl.dCAR.R | 762 +++++++------- R/mcl.glm.R | 178 +-- R/mcl.pois.R | 618 ++++++------ R/postZ.R | 144 +- R/postZsub.R | 2144 +++++++++++++++++++++--------------------- R/rsmMCL.R | 537 +++++----- R/rsmSub.R | 756 +++++++------- R/summary.OptimMCL.HCAR.R |only R/summary.OptimMCL.R | 149 +- R/summary.rsmMCL.R | 145 +- build/partial.rdb |binary data |only inst/doc/mclcar_vignette.Rnw | 646 ++++++------ inst/doc/mclcar_vignette.pdf |binary man/CAR.simLM.Rd | 176 +-- man/OptimMCL.HCAR.Rd |only man/OptimMCL.Rd | 310 +++--- man/ScotCancer.Rd |only man/loglik.dCAR.Rd | 191 +-- man/mcl.HCAR.Rd |only man/mcl.dCAR.Rd | 293 ++--- man/mcl.glm.Rd | 372 +++---- man/mclcar-package.Rd | 166 +-- man/plot.rsmMCL.Rd | 90 - man/postZ.Rd | 222 ++-- man/rsmMCL.Rd | 428 ++++---- man/scotplot.Rd |only man/sim.HCAR.Rd |only man/summary.OptimMCL.HCAR.Rd |only man/summary.OptimMCL.Rd | 106 +- man/summary.rsmMCL.Rd | 120 +- vignettes/mclcar_vignette.Rnw | 646 ++++++------ vignettes/references.bib | 1752 +++++++++++++++++----------------- 43 files changed, 6378 insertions(+), 6325 deletions(-)
Title: Geographically-Weighted Models
Description: In GWmodel, we introduce techniques from a particular branch of spatial statistics,termed geographically-weighted (GW) models. GW models suit situations when data are not described well by some global model, but where there are spatial regions where a suitably localised calibration provides a better description. GWmodel includes functions to calibrate: GW summary statistics, GW principal components analysis, GW discriminant analysis and various forms of GW regression; some of which are provided in basic and robust (outlier resistant) forms.
Author: Binbin Lu[aut], Paul Harris[aut], Martin Charlton[aut], Chris Brunsdon[aut], Tomoki Nakaya[aut], Isabella Gollini[ctb]
Maintainer: Binbin Lu <binbinlu@whu.edu.cn>
Diff between GWmodel versions 1.2-5 dated 2015-02-01 and 2.0-1 dated 2016-11-30
GWmodel-1.2-5/GWmodel/man/check.components.rd |only GWmodel-1.2-5/GWmodel/man/glyph.plot.rd |only GWmodel-1.2-5/GWmodel/man/gwr.generalised.Rd |only GWmodel-1.2-5/GWmodel/man/mink.approach.rd |only GWmodel-1.2-5/GWmodel/man/mink.matrixview.rd |only GWmodel-1.2-5/GWmodel/man/model.selection.gwr.Rd |only GWmodel-1.2-5/GWmodel/man/model.sort.gwr.Rd |only GWmodel-1.2-5/GWmodel/man/model.view.gwr.rd |only GWmodel-1.2-5/GWmodel/man/montecarlo.gwpca.1.rd |only GWmodel-1.2-5/GWmodel/man/montecarlo.gwpca.2.rd |only GWmodel-1.2-5/GWmodel/man/montecarlo.gwr.Rd |only GWmodel-1.2-5/GWmodel/man/montecarlo.gwss.Rd |only GWmodel-1.2-5/GWmodel/man/plot.mcsims.rd |only GWmodel-1.2-5/GWmodel/man/print.ggwrm.Rd |only GWmodel-1.2-5/GWmodel/man/print.gwrm.Rd |only GWmodel-1.2-5/GWmodel/man/print.gwrm.lcr.rd |only GWmodel-1.2-5/GWmodel/man/print.gwrm.pred.rd |only GWmodel-1.2-5/GWmodel/man/print.gwss.Rd |only GWmodel-1.2-5/GWmodel/man/writeGWR.Rd |only GWmodel-1.2-5/GWmodel/man/writeGWR.shp.Rd |only GWmodel-2.0-1/GWmodel/DESCRIPTION | 15 GWmodel-2.0-1/GWmodel/MD5 | 165 +++++----- GWmodel-2.0-1/GWmodel/NAMESPACE | 12 GWmodel-2.0-1/GWmodel/R/GeneralizedGWR.r | 312 ++++++++++++++++---- GWmodel-2.0-1/GWmodel/R/LocalsummaryStatistics.r | 93 ++++- GWmodel-2.0-1/GWmodel/R/Model.selection.r | 220 ++++++++++++-- GWmodel-2.0-1/GWmodel/R/MontCarlo.r | 129 ++++++++ GWmodel-2.0-1/GWmodel/R/RcppExports.R |only GWmodel-2.0-1/GWmodel/R/bw.ggwr.r | 75 ++-- GWmodel-2.0-1/GWmodel/R/bw.gwda.r | 2 GWmodel-2.0-1/GWmodel/R/bw.gwss.average.R |only GWmodel-2.0-1/GWmodel/R/bw.sel.r | 43 +- GWmodel-2.0-1/GWmodel/R/collinearity.r | 11 GWmodel-2.0-1/GWmodel/R/gw.average.cv.R |only GWmodel-2.0-1/GWmodel/R/gw.average.cv.contrib.R |only GWmodel-2.0-1/GWmodel/R/gw.dist.r | 142 +++------ GWmodel-2.0-1/GWmodel/R/gw.weight.r | 136 ++++---- GWmodel-2.0-1/GWmodel/R/gwda.r | 4 GWmodel-2.0-1/GWmodel/R/gwpca.mc.r | 77 ++++ GWmodel-2.0-1/GWmodel/R/gwpca.r | 2 GWmodel-2.0-1/GWmodel/R/gwpca.visualization.r | 73 ++++ GWmodel-2.0-1/GWmodel/R/gwr.basic.r | 233 ++++++++++---- GWmodel-2.0-1/GWmodel/R/gwr.collin.diagno.r | 2 GWmodel-2.0-1/GWmodel/R/gwr.hetero.r | 10 GWmodel-2.0-1/GWmodel/R/gwr.mixed.r | 49 +-- GWmodel-2.0-1/GWmodel/R/gwr.predict.r | 8 GWmodel-2.0-1/GWmodel/R/gwr.robust.r | 8 GWmodel-2.0-1/GWmodel/R/gwr.t.adjust.r | 4 GWmodel-2.0-1/GWmodel/R/mink.pvals.R |only GWmodel-2.0-1/GWmodel/R/minkovski.approach.r | 250 ++++++++++++++-- GWmodel-2.0-1/GWmodel/R/writeGWR.r | 28 + GWmodel-2.0-1/GWmodel/R/zzz.r | 5 GWmodel-2.0-1/GWmodel/inst/CITATION | 19 + GWmodel-2.0-1/GWmodel/man/EWHP.Rd | 2 GWmodel-2.0-1/GWmodel/man/EWOutline.rd | 4 GWmodel-2.0-1/GWmodel/man/GWmodel-package.Rd | 11 GWmodel-2.0-1/GWmodel/man/Georgia.Rd | 2 GWmodel-2.0-1/GWmodel/man/GeorgiaCounties.rd | 4 GWmodel-2.0-1/GWmodel/man/LondonHP.Rd | 2 GWmodel-2.0-1/GWmodel/man/USelect.rd | 9 GWmodel-2.0-1/GWmodel/man/bw.ggwr.Rd | 15 GWmodel-2.0-1/GWmodel/man/bw.gwda.rd | 19 - GWmodel-2.0-1/GWmodel/man/bw.gwpca.rd | 18 + GWmodel-2.0-1/GWmodel/man/bw.gwr.Rd | 4 GWmodel-2.0-1/GWmodel/man/bw.gwr.lcr.rd | 20 + GWmodel-2.0-1/GWmodel/man/bw.gwss.average.Rd |only GWmodel-2.0-1/GWmodel/man/ggwr.basic.Rd |only GWmodel-2.0-1/GWmodel/man/ggwr.cv.Rd | 3 GWmodel-2.0-1/GWmodel/man/ggwr.cv.contrib.Rd | 3 GWmodel-2.0-1/GWmodel/man/gw.dist.Rd | 19 - GWmodel-2.0-1/GWmodel/man/gw.pcplot.rd | 6 GWmodel-2.0-1/GWmodel/man/gw.weight.Rd |only GWmodel-2.0-1/GWmodel/man/gwda.rd | 8 GWmodel-2.0-1/GWmodel/man/gwpca.check.components.rd |only GWmodel-2.0-1/GWmodel/man/gwpca.cv.Rd | 3 GWmodel-2.0-1/GWmodel/man/gwpca.cv.contrib.Rd | 3 GWmodel-2.0-1/GWmodel/man/gwpca.glyph.plot.rd |only GWmodel-2.0-1/GWmodel/man/gwpca.montecarlo.1.rd |only GWmodel-2.0-1/GWmodel/man/gwpca.montecarlo.2.rd |only GWmodel-2.0-1/GWmodel/man/gwpca.rd | 12 GWmodel-2.0-1/GWmodel/man/gwr.basic.rd | 31 - GWmodel-2.0-1/GWmodel/man/gwr.collin.diagno.Rd | 4 GWmodel-2.0-1/GWmodel/man/gwr.cv.Rd | 3 GWmodel-2.0-1/GWmodel/man/gwr.cv.contrib.Rd | 3 GWmodel-2.0-1/GWmodel/man/gwr.hetero.rd | 4 GWmodel-2.0-1/GWmodel/man/gwr.lcr.cv.Rd | 3 GWmodel-2.0-1/GWmodel/man/gwr.lcr.cv.contrib.Rd | 3 GWmodel-2.0-1/GWmodel/man/gwr.lcr.rd | 5 GWmodel-2.0-1/GWmodel/man/gwr.mink.approach.rd |only GWmodel-2.0-1/GWmodel/man/gwr.mink.matrixview.rd |only GWmodel-2.0-1/GWmodel/man/gwr.mink.pval.rd |only GWmodel-2.0-1/GWmodel/man/gwr.mixed.rd | 11 GWmodel-2.0-1/GWmodel/man/gwr.model.selection.Rd |only GWmodel-2.0-1/GWmodel/man/gwr.model.sort.Rd |only GWmodel-2.0-1/GWmodel/man/gwr.model.view.rd |only GWmodel-2.0-1/GWmodel/man/gwr.montecarlo.Rd |only GWmodel-2.0-1/GWmodel/man/gwr.predict.Rd | 14 GWmodel-2.0-1/GWmodel/man/gwr.robust.Rd | 5 GWmodel-2.0-1/GWmodel/man/gwr.t.adjust.rd | 2 GWmodel-2.0-1/GWmodel/man/gwr.write.Rd |only GWmodel-2.0-1/GWmodel/man/gwss.montecarlo.Rd |only GWmodel-2.0-1/GWmodel/man/gwss.rd | 8 GWmodel-2.0-1/GWmodel/src |only 103 files changed, 1760 insertions(+), 630 deletions(-)
Title: Coclustering Package for Binary, Categorical, Contingency and
Continuous Data-Sets
Description: Simultaneous clustering of rows and columns, usually designated by
biclustering, co-clustering or block clustering, is an important technique
in two way data analysis. It consists of estimating a mixture model which
takes into account the block clustering problem on both the individual and
variables sets. The blockcluster package provides a bridge between the C++
core library and the R statistical computing environment. This package
allows to co-cluster binary, contingency, continuous and categorical
data-sets. It also provides utility functions to visualize the results.
This package may be useful for various applications in fields of Data
mining, Information retrieval, Biology, computer vision and many more. More
information about the project and comprehensive tutorial can be found on
the link mentioned in URL.
Author: Serge Iovleff [aut, cre],
Parmeet Singh Bhatia [aut],
Josselin Demont [ctb],
Gerard Goavert [ctb],
Vincent Brault [ctb],
Christophe Biernacki [ctb],
Gilles Celeux [ctb]
Maintainer: Serge Iovleff <Serge.Iovleff@stkpp.org>
Diff between blockcluster versions 4.2.0 dated 2016-11-29 and 4.2.1 dated 2016-11-30
DESCRIPTION | 6 +++--- MD5 | 6 +++--- inst/doc/blockcluster_tutorial.pdf |binary src/Makevars.win | 15 ++++++++++++--- 4 files changed, 18 insertions(+), 9 deletions(-)
Title: Tools for Conducting Respirometry Experiments
Description: Provides tools to enable the researcher to more precisely conduct
respirometry experiments. Strong emphasis is on aquatic respirometry. Tools
focus on helping the researcher setup and conduct experiments. Analysis of the
resulting data is not a focus since analyses are often specific to a particular
setup, and thus are better created by the researcher individually. This
package provides tools for intermittent, flow-through, and closed respirometry
techniques.
Author: Matthew A. Birk
Maintainer: Matthew A. Birk <matthewabirk@gmail.com>
Diff between respirometry versions 0.2.0 dated 2016-10-08 and 0.3.0 dated 2016-11-30
DESCRIPTION | 12 ++++---- MD5 | 59 +++++++++++++++++++++++----------------- NAMESPACE | 4 ++ NEWS | 32 +++++++++++++++------ R/Q10.R | 28 +++++++++--------- R/RQ.R | 8 ++--- R/calc_MO2.R |only R/calc_b.R |only R/closed.R | 9 +++--- R/co2_flush.R | 4 +- R/conv_o2.R | 8 +++++ R/conv_resp_unit.R |only R/flush_o2.R | 25 ++++++++-------- R/flush_water.R | 13 ++++---- R/import_firesting.R |only R/import_presens.R | 19 ++++++------ R/import_witrox.R | 30 ++++++++++---------- R/max_MO2.R | 2 - R/predict_pH.R | 18 ------------ R/scale_MO2.R | 27 ++++++++---------- inst/extdata/firesting_file.txt |only man/Q10.Rd | 16 +++++----- man/RQ.Rd | 8 ++--- man/calc_MO2.Rd |only man/calc_b.Rd |only man/closed.Rd | 11 ++++--- man/co2_flush.Rd | 2 - man/conv_o2.Rd | 2 + man/conv_resp_unit.Rd |only man/flush_water.Rd | 4 +- man/import_firesting.Rd |only man/import_presens.Rd | 6 ++-- man/import_witrox.Rd | 11 ++----- man/max_MO2.Rd | 2 - man/scale_MO2.Rd | 18 ++++++------ 35 files changed, 201 insertions(+), 177 deletions(-)
Title: Iterator Based Expression Template Expansion of Standard
Operators
Description: Creates an easy way to use expression templates with R
semantics on any iterator based structure.
Author: Daniel C. Dillon
Maintainer: Daniel C. Dillon <dcdillon@gmail.com>
Diff between RcppHoney versions 0.1.2 dated 2016-11-26 and 0.1.4 dated 2016-11-30
DESCRIPTION | 6 ++-- MD5 | 16 +++++------ R/plugin.R | 59 ++++++++++++++++++++++++++++++++++++++----- build/vignette.rds |binary inst/doc/functions.Rmd | 2 - inst/doc/functions.html | 4 +- inst/doc/introduction.html | 4 +- inst/tools/stripper | 61 ++++++++++++++++++++++++++------------------- vignettes/functions.Rmd | 2 - 9 files changed, 105 insertions(+), 49 deletions(-)
Title: Monte-Carlo Methods for Prediction Functions
Description: Marginalizes prediction functions using Monte-Carlo integration and computes permutation importance.
Author: Zachary Jones [aut, cre]
Maintainer: Zachary Jones <zmj@zmjones.com>
Diff between mmpf versions 0.0.1 dated 2016-11-11 and 0.0.2 dated 2016-11-30
DESCRIPTION | 12 - MD5 | 24 +- NAMESPACE | 1 R/grid.R | 54 ++--- R/mp.R | 28 +- build/vignette.rds |binary inst/doc/mmpf.R | 41 +++- inst/doc/mmpf.Rmd | 64 ++++-- inst/doc/mmpf.html | 427 ++++++++++++++++++++++++++++++--------------- man/makeDesign.Rd | 4 man/marginalPrediction.Rd | 12 - tests/testthat/test_grid.R | 4 vignettes/mmpf.Rmd | 64 ++++-- 13 files changed, 487 insertions(+), 248 deletions(-)
Title: Probabilistic Population Projection
Description: Generating population projections for all countries of the world using several probabilistic components, such as total fertility rate and life expectancy.
Author: Hana Sevcikova, Adrian Raftery, Thomas Buettner
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between bayesPop versions 6.0-2 dated 2016-11-22 and 6.0-3 dated 2016-11-30
ChangeLog | 8 ++++++++ DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- NAMESPACE | 4 +++- R/get_outputs.R | 39 ++++++++++++++++++++++++++++++++++----- inst/CITATION |only man/bayesPop-package.Rd | 8 ++++++-- man/expressions.Rd | 6 ++++++ man/get.pop.Rd | 27 ++++++++++++++++++++------- man/pop.aggregate.Rd | 6 ++++++ man/predict.pop.Rd | 4 ++++ 11 files changed, 101 insertions(+), 28 deletions(-)