Title: A set of tools for working with list objects
Diff between rlist versions 0.2.4 dated 2014-07-26 and 0.2.5 dated 2014-07-31
Description: A set of tools for working with lists as dataset,
including filtering, mapping, grouping, sorting, updating,
searching, and many other functions. It recommends functional
programming and collection pipeline in list operations.
Author: Kun Ren
Maintainer: Kun Ren
DESCRIPTION | 16 ++++++------
MD5 | 47 ++++++++++++++++++++++----------------
NAMESPACE | 9 +++++++
NEWS | 8 ++++++
R/functions.R | 5 +++-
R/list.apply.R |only
R/list.clean.R | 11 +++++++-
R/list.load.R | 3 --
R/list.search.R |only
README.md | 9 +++----
build/vignette.rds |binary
inst/doc/Examples.html | 3 --
inst/doc/Filtering.html | 3 --
inst/doc/Grouping.html | 3 --
inst/doc/IO.html | 3 --
inst/doc/Introduction.html | 11 --------
inst/doc/Joining.html | 3 --
inst/doc/Lambda.html | 3 --
inst/doc/Mapping.html | 3 --
inst/doc/Searching.R |only
inst/doc/Searching.html |only
inst/doc/Sorting.html | 3 --
inst/doc/Updating.html | 3 --
man/exact-search.Rd |only
man/fuzzy-search.Rd |only
man/list.apply.Rd |only
man/list.clean.Rd | 5 +++-
man/list.search.Rd |only
tests/testthat/test-list.search.R |only
29 files changed, 76 insertions(+), 75 deletions(-)
Title: Learned Pattern Similarity and Representation for Time Series
Diff between LPStimeSeries versions 1.0-2 dated 2014-03-23 and 1.0-3 dated 2014-07-31
Description: Learned Pattern Similarity (LPS) for time series. This package is based on the
'randomForest' package by Andy Liaw. LPS aims at finding time series patterns to
compute the similarity.
Author: Learned Pattern Similarity (LPS) for time series by Mustafa Gokce Baydogan,
Ensemble of regression trees by Andy Liaw and Matthew Wiener.
Maintainer: Mustafa Gokce Baydogan
DESCRIPTION | 6
MD5 | 36 ++---
R/computeSimilarity.R | 14 +-
R/getTreeInfo.R | 3
R/learnPattern.default.R | 19 ++
R/predict.learnPattern.R | 22 ++-
R/tunelearnPattern.R | 12 -
inst/CITATION | 5
inst/NEWS | 31 ++++
man/computeSimilarity.Rd | 7 -
man/getTreeInfo.Rd | 1
man/learnPattern.Rd | 29 +++-
man/plotMDS.Rd | 5
man/predict.learnPattern.Rd | 25 ++-
man/tunelearnPattern.Rd | 6
src/regTree.c | 165 +++++++++++++-----------
src/regrf.c | 292 ++++++++++++++++++++------------------------
src/rf.h | 17 +-
src/rfutils.c | 50 +++++++
19 files changed, 454 insertions(+), 291 deletions(-)
Title: Statistical Analysis of Point Processes
Diff between SAPP versions 1.0.3 dated 2013-07-24 and 1.0.4 dated 2014-07-31
Description: Functions for statistical analysis of point processes.
Author: The Institute of Statistical Mathematics
Maintainer: Masami Saga
DESCRIPTION | 6 +++---
MD5 | 20 ++++++++++----------
data/Brastings.rda |binary
data/PProcess.rda |binary
data/PoissonData.rda |binary
data/SelfExcit.rda |binary
data/main2003JUL26.rda |binary
data/res2003JUL26.rda |binary
inst/doc/SAPP-manual.pdf |binary
inst/doc/changes.txt | 5 +++++
inst/doc/index.html | 45 ++++++++++++++++++---------------------------
11 files changed, 36 insertions(+), 40 deletions(-)
Title: MultiVariate Stochastic Linear Ornstein-Uhlenbeck models for
phylogenetic Comparative hypotHeses
Diff between mvSLOUCH versions 1.1.2 dated 2014-07-21 and 1.1.3 dated 2014-07-31
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history.
Author: Krzysztof Bartoszek
Maintainer: Krzysztof Bartoszek
DESCRIPTION | 6 +--
MD5 | 28 ++++++++--------
R/PhyloSDEestim.R | 3 +
R/ci.R | 2 -
R/estimBM.R | 5 ++-
R/estimGLSGC.R | 1
R/modelparams.R | 9 ++++-
R/modelparamstransform.R | 1
R/phylgls.R | 65 +++++++++++++++++++++------------------
R/precalcs.R | 17 ++++++----
R/simulVasicekprocphyl.R | 11 ++++++
R/wrappers.R | 12 +++----
man/simulBMProcPhylTree.Rd | 25 +++++++++++++--
man/simulMVSLOUCHProcPhylTree.Rd | 21 ++++++++++++
man/simulOUCHProcPhylTree.Rd | 14 +++++++-
15 files changed, 150 insertions(+), 70 deletions(-)
Title: Fractional Factorial designs with 2-level factors
Diff between FrF2 versions 1.7 dated 2014-02-27 and 1.7-1 dated 2014-07-31
Description: This package creates regular and non-regular Fractional
Factorial designs. Furthermore, analysis tools for Fractional
Factorial designs with 2-level factors are offered (main
effects and interaction plots for all factors simultaneously,
cube plot for looking at the simultaneous effects of three
factors, full or half normal plot, alias structure in a more
readable format than with the built-in function alias). The
package is still under development. While much of the intended
functionality is already available, some changes and
improvements are still to be expected. Suggestions are welcome.
Author: Ulrike Groemping
Maintainer: Ulrike Groemping
DESCRIPTION | 10 +++++-----
MD5 | 22 +++++++++++-----------
NAMESPACE | 2 +-
R/IAPlot.R | 4 ++++
R/MEPlot.R | 2 ++
R/sysdata.rda |binary
inst/NEWS | 13 +++++++++++++
man/CIG.Rd | 4 ++--
man/DanielPlot.Rd | 4 ++++
man/FrF2-package.Rd | 4 +++-
man/FrF2.Rd | 2 +-
man/IAPlot.Rd | 11 +++++++++--
12 files changed, 55 insertions(+), 23 deletions(-)
Title: An Efficient Swiss Army Knife for Population Genomic Analyses
Diff between PopGenome versions 2.0.7 dated 2014-05-19 and 2.0.8 dated 2014-07-31
Description: PopGenome is an R-package for Population Genetic & Genomic Analysis
Author: Bastian Pfeifer, Ulrich Wittelsbuerger
Maintainer: Bastian Pfeifer
PopGenome-2.0.7/PopGenome/vignettes/PopGenome_classes.pdf |only
PopGenome-2.0.7/PopGenome/vignettes/icon_PopGenome_transparent.png |only
PopGenome-2.0.8/PopGenome/DESCRIPTION | 8
PopGenome-2.0.8/PopGenome/MD5 | 85 -
PopGenome-2.0.8/PopGenome/NAMESPACE | 1
PopGenome-2.0.8/PopGenome/NEWS | 19
PopGenome-2.0.8/PopGenome/R/GENOME.R | 48
PopGenome-2.0.8/PopGenome/R/PopGenread.R | 42
PopGenome-2.0.8/PopGenome/R/calc_D.R |only
PopGenome-2.0.8/PopGenome/R/calc_diversities.R | 13
PopGenome-2.0.8/PopGenome/R/calc_hwhafsth.R | 4
PopGenome-2.0.8/PopGenome/R/concatenate.R | 1
PopGenome-2.0.8/PopGenome/R/get_data.R | 11
PopGenome-2.0.8/PopGenome/R/introgression.stats.R |only
PopGenome-2.0.8/PopGenome/R/myReadVCF.R |only
PopGenome-2.0.8/PopGenome/R/readData.R | 11
PopGenome-2.0.8/PopGenome/R/readVCF.R | 5
PopGenome-2.0.8/PopGenome/R/readVCFchunk.R | 423 ++++++++
PopGenome-2.0.8/PopGenome/R/save_load_GENOME.R | 124 +-
PopGenome-2.0.8/PopGenome/R/set.synnonsyn.R | 4
PopGenome-2.0.8/PopGenome/inst/CITATION |only
PopGenome-2.0.8/PopGenome/inst/doc/An_introduction_to_the_PopGenome_package.Rnw | 515 +++++-----
PopGenome-2.0.8/PopGenome/inst/doc/An_introduction_to_the_PopGenome_package.pdf |binary
PopGenome-2.0.8/PopGenome/inst/doc/Integration_of_new_Methods.Rnw | 2
PopGenome-2.0.8/PopGenome/inst/doc/Integration_of_new_Methods.pdf |binary
PopGenome-2.0.8/PopGenome/man/F_ST.stats-methods.Rd | 11
PopGenome-2.0.8/PopGenome/man/GENOME-class.Rd | 4
PopGenome-2.0.8/PopGenome/man/calc.R2-methods.Rd | 4
PopGenome-2.0.8/PopGenome/man/diversity.stats-methods.Rd | 8
PopGenome-2.0.8/PopGenome/man/get.codons-methods.Rd | 10
PopGenome-2.0.8/PopGenome/man/introgression.stats.Rd |only
PopGenome-2.0.8/PopGenome/man/linkage.stats-methods.Rd | 3
PopGenome-2.0.8/PopGenome/man/load.session.Rd | 8
PopGenome-2.0.8/PopGenome/man/readData.Rd | 11
PopGenome-2.0.8/PopGenome/man/readVCF.Rd | 14
PopGenome-2.0.8/PopGenome/man/save.session.Rd | 9
PopGenome-2.0.8/PopGenome/man/set.populations-methods.Rd | 6
PopGenome-2.0.8/PopGenome/man/set.synnonsyn-methods.Rd | 24
PopGenome-2.0.8/PopGenome/src/Makevars | 2
PopGenome-2.0.8/PopGenome/src/Makevars.win | 2
PopGenome-2.0.8/PopGenome/src/myReadVCFC.c |only
PopGenome-2.0.8/PopGenome/src/whopgenome/readdnapp.cpp | 2
PopGenome-2.0.8/PopGenome/src/whopgenome/whopgen_codemat.cpp | 449 ++++++++
PopGenome-2.0.8/PopGenome/vignettes/An_introduction_to_the_PopGenome_package.Rnw | 515 +++++-----
PopGenome-2.0.8/PopGenome/vignettes/Integration_of_new_Methods.Rnw | 2
PopGenome-2.0.8/PopGenome/vignettes/PopGenomeClasses.pdf |only
PopGenome-2.0.8/PopGenome/vignettes/XXX.pdf |binary
PopGenome-2.0.8/PopGenome/vignettes/XYZ.pdf |binary
48 files changed, 1708 insertions(+), 692 deletions(-)
Title: Multiple Aggregation Prediction Algorithm
Diff between MAPA versions 1.6 dated 2014-07-03 and 1.7 dated 2014-07-31
Description: This package contains functions and wrappers for using the Multiple Aggregation Prediction Algorithm, proposed by Kourentzes et al. (2014).
Author: Nikolaos Kourentzes and Fotios Petropoulos
Maintainer: Nikolaos Kourentzes
ChangeLog | 19 ++++++---
DESCRIPTION | 10 ++---
MD5 | 15 ++++---
NAMESPACE | 4 +-
R/MAPA.R | 106 +++++++++++++++++++++++++++++++++++++++++++++++-------
man/mapa.Rd | 2 -
man/mapaest.Rd | 2 -
man/mapasimple.Rd | 2 -
man/plotmapa.Rd |only
9 files changed, 124 insertions(+), 36 deletions(-)
Title: CRAN Task Views
Diff between ctv versions 0.7-9 dated 2014-01-05 and 0.8-0 dated 2014-07-31
Description: Server-side and client-side tools for task views
to CRAN-style repositories
Author: Achim Zeileis [aut, cre],
Kurt Hornik [aut]
Maintainer: Achim Zeileis
DESCRIPTION | 8
MD5 | 101 +
NEWS | 6
R/ctv-server.R | 132 +-
build/vignette.rds |binary
inst/ctv/Bayesian.ctv | 91 -
inst/ctv/Bayesian.html |only
inst/ctv/ChemPhys.ctv | 67 -
inst/ctv/ChemPhys.html |only
inst/ctv/ClinicalTrials.ctv | 17
inst/ctv/ClinicalTrials.html |only
inst/ctv/Cluster.ctv | 70 -
inst/ctv/Cluster.html |only
inst/ctv/DifferentialEquations.html |only
inst/ctv/Distributions.ctv | 1932 ++++++++++++++++----------------
inst/ctv/Distributions.html |only
inst/ctv/Econometrics.ctv | 9
inst/ctv/Econometrics.html |only
inst/ctv/Environmetrics.ctv | 48
inst/ctv/Environmetrics.html |only
inst/ctv/ExperimentalDesign.ctv | 6
inst/ctv/ExperimentalDesign.html |only
inst/ctv/Finance.ctv | 74 -
inst/ctv/Finance.html |only
inst/ctv/Genetics.ctv | 5
inst/ctv/Genetics.html |only
inst/ctv/Graphics.html |only
inst/ctv/HighPerformanceComputing.ctv | 29
inst/ctv/HighPerformanceComputing.html |only
inst/ctv/MachineLearning.ctv | 40
inst/ctv/MachineLearning.html |only
inst/ctv/MedicalImaging.html |only
inst/ctv/MetaAnalysis.ctv | 190 ++-
inst/ctv/MetaAnalysis.html |only
inst/ctv/Multivariate.ctv | 14
inst/ctv/Multivariate.html |only
inst/ctv/NaturalLanguageProcessing.ctv | 29
inst/ctv/NaturalLanguageProcessing.html |only
inst/ctv/NumericalMathematics.ctv | 48
inst/ctv/NumericalMathematics.html |only
inst/ctv/OfficialStatistics.ctv | 82 -
inst/ctv/OfficialStatistics.html |only
inst/ctv/Optimization.ctv | 28
inst/ctv/Optimization.html |only
inst/ctv/Pharmacokinetics.ctv | 6
inst/ctv/Pharmacokinetics.html |only
inst/ctv/Phylogenetics.ctv | 100 +
inst/ctv/Phylogenetics.html |only
inst/ctv/Psychometrics.ctv | 78 -
inst/ctv/Psychometrics.html |only
inst/ctv/ReproducibleResearch.ctv | 63 -
inst/ctv/ReproducibleResearch.html |only
inst/ctv/Robust.ctv | 87 +
inst/ctv/Robust.html |only
inst/ctv/SocialSciences.ctv | 6
inst/ctv/SocialSciences.html |only
inst/ctv/Spatial.ctv | 69 -
inst/ctv/Spatial.html |only
inst/ctv/SpatioTemporal.ctv | 7
inst/ctv/SpatioTemporal.html |only
inst/ctv/Survival.ctv | 310 +++--
inst/ctv/Survival.html |only
inst/ctv/TimeSeries.ctv | 153 +-
inst/ctv/TimeSeries.html |only
inst/ctv/WebTechnologies.ctv | 405 ++++--
inst/ctv/WebTechnologies.html |only
inst/ctv/gR.html |only
inst/doc/ctv-howto.pdf |binary
68 files changed, 2535 insertions(+), 1775 deletions(-)
Title: Some Tools for Survey Statistics in Educational Assessment,
Developed by BIFIE
Diff between BIFIEsurvey versions 0.2-37 dated 2014-07-12 and 0.3-47 dated 2014-07-31
Description:
Some Tools for Survey Statistics in Educational Assessment,
Developed by BIFIE.
Bundesinstitut fuer Bildungsforschung,
Entwicklung und Innovation im oesterreichischen Schulwesen;
Federal Institute for Educational Research, Innovation and
Development of the Austrian School System;
Salzburg, Austria.
Author: BIFIE
Maintainer: Alexander Robitzsch
DESCRIPTION | 12 -
MD5 | 69 ++++---
NAMESPACE | 13 +
R/BIFIE.bifiedata2bifiecdata.R |only
R/BIFIE.by.R | 8
R/BIFIE.correl.R | 17 +
R/BIFIE.crosstab.R | 14 -
R/BIFIE.data.R | 83 ++++++++-
R/BIFIE.data.boot.R |only
R/BIFIE.data.jack.R | 91 ++++++----
R/BIFIE.data.select.R |only
R/BIFIE.data.transform.R | 126 +++++++++++--
R/BIFIE.ecdf.R | 4
R/BIFIE.freq.R | 6
R/BIFIE.hist.R | 4
R/BIFIE.linreg.R | 20 +-
R/BIFIE.logistreg.R |only
R/BIFIE.mva.R |only
R/BIFIE.univar.R | 21 +-
R/BIFIE.waldtest.R | 7
R/cdata.wgtrep.R |only
R/load.BIFIE.data.R |only
R/load.BIFIEdata.files.R |only
R/save.BIFIE.data.R |only
R/write.BIFIE.data.R |only
data/data.timss1.ind.rda |only
data/datalist | 1
inst/NEWS | 63 +++++-
man/BIFIE.BIFIEdata2BIFIEcdata.Rd |only
man/BIFIE.data.Rd | 45 ++++
man/BIFIE.data.boot.Rd |only
man/BIFIE.data.jack.Rd | 40 +++-
man/BIFIE.data.select.Rd |only
man/BIFIE.data.transform.Rd | 132 +++++++++++++-
man/BIFIE.logistreg.Rd |only
man/BIFIE.mva.Rd |only
man/BIFIE.waldtest.Rd | 5
man/BIFIEsurvey-package.Rd | 98 +++++++---
man/data.pisaNLD.Rd | 10 -
man/data.timss1.Rd | 14 -
man/save.BIFIEdata.Rd |only
src/jack_dataprep.cpp | 345 ++++++++++++++++++++++++++++++++++++++
src/univar.cpp | 193 +++++++++++++++++++++
src/univar_helpers.h | 106 +++++++++++
44 files changed, 1343 insertions(+), 204 deletions(-)
Title: TIMe Series Analysis and Control package
Diff between timsac versions 1.3.2 dated 2014-06-02 and 1.3.3 dated 2014-07-31
Description: Functions for statistical analysis, prediction and control of time series.
Author: The Institute of Statistical Mathematics
Maintainer: Masami Saga
DESCRIPTION | 8 +++-----
MD5 | 26 +++++++++++++-------------
data/Airpollution.rda |binary
data/Amerikamaru.rda |binary
data/Blsallfood.rda |binary
data/Canadianlynx.rda |binary
data/LaborData.rda |binary
data/Powerplant.rda |binary
data/bispecData.rda |binary
data/locarData.rda |binary
data/nonstData.rda |binary
inst/doc/changes.txt | 5 +++++
inst/doc/index.html | 27 ++++++++++++++++-----------
inst/doc/timsac-manual.pdf |binary
14 files changed, 37 insertions(+), 29 deletions(-)
Title: Visualization of spatial and spatio-temporal objects in Google
Earth
Diff between plotKML versions 0.4-4 dated 2014-05-04 and 0.4-5 dated 2014-07-31
Description: Writes sp-class, spacetime-class, raster-class and similar spatial and spatio-temporal objects to KML following some basic cartographic rules.
Author: Tomislav Hengl [cre, aut],
Pierre Roudier [ctb],
Dylan Beaudette [ctb],
Edzer Pebesma [ctb],
Michael Blaschek [ctb]
Maintainer: Tomislav Hengl
DESCRIPTION | 8 +-
MD5 | 48 +++++++++++-----
NAMESPACE | 6 +-
R/AAAA.R | 91 ++++++++++++++++++++++---------
R/layer.STTDF.R | 2
R/layer.SpatialLines.R | 2
R/layer.SpatialPoints.R | 2
R/layer.SpatialPolygons.R | 2
R/legend.bar.R | 2
R/plot.SpatialPredictions.R |only
R/plotKML.SpatialPredictions.R | 38 +++---------
build |only
inst/doc |only
man/HRtemp08.Rd | 120 ++++++++++++++++++++++++++++++++++++-----
man/SpatialPredictions.Rd | 3 +
man/baranja.Rd | 11 ++-
man/layer.STIDF.Rd | 2
man/layer.SpatialPoints.Rd | 13 ++++
vignettes |only
19 files changed, 252 insertions(+), 98 deletions(-)
Title: Bayesian fitting of Ornstein-Uhlenbeck models to phylogenies
Diff between bayou versions 1.0 dated 2014-07-18 and 1.0.1 dated 2014-07-31
Description: Tools for fitting and simulating multi-optima Ornstein-Uhlenbeck
models to phylogenetic comparative data using Bayesian reversible-jump
methods.
Author: Josef C. Uyeda, Jon Eastman and Luke Harmon
Maintainer: Josef C. Uyeda
DESCRIPTION | 8 ++++----
MD5 | 3 ++-
src/Makevars.win |only
3 files changed, 6 insertions(+), 5 deletions(-)
Title: The YUIMA Project package for SDEs
Diff between yuima versions 1.0.21 dated 2014-05-05 and 1.0.24 dated 2014-07-31
Description: Simulation and Inference for Stochastic Differential Equations
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus
DESCRIPTION | 10
MD5 | 16
NEWS | 8
R/WoodChanfGn.R | 8
R/llag.R | 910 +++++++++++++++++++++++++++++++---------------------
R/yuima.R | 13
R/yuima.sampling.R | 26 +
man/llag.Rd | 44 +-
src/cce_functions.c | 100 ++++-
9 files changed, 696 insertions(+), 439 deletions(-)
Title: Computation of generalized Nash equilibria
Diff between GNE versions 0.98 dated 2014-06-11 and 0.99-0 dated 2014-07-31
Description: Provide functions to compute standard and generalized Nash Equilibria. The following optimization methods are available nonsmooth reformulation, fixed-point formulation, minimization problem and constrained-equation reformulation.
Author: Christophe Dutang
Maintainer: Christophe Dutang
GNE-0.98/GNE/man/eqsolve.Rd |only
GNE-0.99-0/GNE/DESCRIPTION | 10 +++++-----
GNE-0.99-0/GNE/MD5 | 27 +++++++++++++--------------
GNE-0.99-0/GNE/R/solv-eq.R | 7 ++++---
GNE-0.99-0/GNE/build/vignette.rds |binary
GNE-0.99-0/GNE/inst/NEWS | 8 ++++++++
GNE-0.99-0/GNE/inst/doc/GNE-howto.Rnw | 4 ++--
GNE-0.99-0/GNE/inst/doc/GNE-howto.pdf |binary
GNE-0.99-0/GNE/man/GNE.Rd | 8 ++++++--
GNE-0.99-0/GNE/man/GNE.ceq.Rd | 2 +-
GNE-0.99-0/GNE/man/GNE.fpeq.Rd | 6 +++---
GNE-0.99-0/GNE/man/GNE.minpb.Rd | 4 ++--
GNE-0.99-0/GNE/man/GNE.nseq.Rd | 2 +-
GNE-0.99-0/GNE/src/SSR.c | 27 +++++++++++++++++++++------
GNE-0.99-0/GNE/vignettes/GNE-howto.Rnw | 4 ++--
15 files changed, 68 insertions(+), 41 deletions(-)
Title: Weighted k-means Clustering
Diff between wskm versions 1.4.7 dated 2014-06-02 and 1.4.11 dated 2014-07-31
Description: Entropy weighted k-means (ewkm) is a weighted subspace
clustering algorithm that is well suited to very high
dimensional data. Weights are calculated as the importance of a
variable with regard to cluster membership.
The two-level variable weighting clustering algorithm TW-k-means (twkm)
introduces two types of weights, the weights on individual variables and
the weights on variable groups, and they are calculated during the clustering process.
The feature group weighted k-means (fgkm) extends this concept by grouping
features and weighting the group in addition to weighting
individual features.
Author: Graham Williams [aut],
Joshua Z Huang [aut],
Xiaojun Chen [aut],
Qiang Wang [aut],
Longfei Xiao [aut],
He Zhao [cre]
Maintainer: He Zhao
DESCRIPTION | 8 ++++----
MD5 | 26 +++++++++++++-------------
R/ewkm.R | 24 ++++++++++++++++++------
R/fgkm.R | 25 +++++++++++++++++++------
R/twkm.R | 23 ++++++++++++++++++-----
inst/ChangeLog | 6 ++++++
man/ewkm.Rd | 7 ++++---
man/fgkm.Rd | 6 ++++--
man/plot.ewkm.Rd | 2 +-
man/twkm.Rd | 6 ++++--
src/ewkm.c | 21 +++++++++++++--------
src/fgkm.c | 9 +++++----
src/twkm.c | 9 +++++----
tests/ewkm01.Rout.save | 10 +++++-----
14 files changed, 119 insertions(+), 63 deletions(-)
Title: Interface to the Global Biodiversity Information Facility API
Diff between rgbif versions 0.6.2 dated 2014-04-24 and 0.7.0 dated 2014-07-31
Description: A programmatic interface to the
Web Service methods provided by the Global
Biodiversity Information Facility.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut],
Vijay Barve [aut],
Dan Mcglinn [aut]
Maintainer: Scott Chamberlain
rgbif-0.6.2/rgbif/inst/doc/rgbif_vignette.pdf |only
rgbif-0.6.2/rgbif/inst/doc/rgbif_vignette_oldapi.pdf |only
rgbif-0.6.2/rgbif/vignettes/rgbif_vignette.html |only
rgbif-0.6.2/rgbif/vignettes/rgbif_vignette.md |only
rgbif-0.6.2/rgbif/vignettes/rgbif_vignette_oldapi.html |only
rgbif-0.6.2/rgbif/vignettes/rgbif_vignette_oldapi.md |only
rgbif-0.7.0/rgbif/DESCRIPTION | 17
rgbif-0.7.0/rgbif/LICENSE |only
rgbif-0.7.0/rgbif/MD5 | 240 ++---
rgbif-0.7.0/rgbif/NAMESPACE | 19
rgbif-0.7.0/rgbif/NEWS | 66 +
rgbif-0.7.0/rgbif/R/check_wkt.r | 19
rgbif-0.7.0/rgbif/R/count_facet.r | 5
rgbif-0.7.0/rgbif/R/dataset_metrics.r | 6
rgbif-0.7.0/rgbif/R/dataset_search.r | 113 +-
rgbif-0.7.0/rgbif/R/dataset_suggest.r | 18
rgbif-0.7.0/rgbif/R/datasets.r | 17
rgbif-0.7.0/rgbif/R/deprecated.r | 24
rgbif-0.7.0/rgbif/R/elevation.r | 2
rgbif-0.7.0/rgbif/R/gbif_photos.r |only
rgbif-0.7.0/rgbif/R/gbifmap.r | 4
rgbif-0.7.0/rgbif/R/installations.r | 45 -
rgbif-0.7.0/rgbif/R/name_backbone.r | 7
rgbif-0.7.0/rgbif/R/name_lookup.r | 56 -
rgbif-0.7.0/rgbif/R/name_suggest.r | 51 -
rgbif-0.7.0/rgbif/R/name_usage.r | 35
rgbif-0.7.0/rgbif/R/networks.r | 13
rgbif-0.7.0/rgbif/R/nodes.r | 18
rgbif-0.7.0/rgbif/R/occ_count.r | 35
rgbif-0.7.0/rgbif/R/occ_get.r | 4
rgbif-0.7.0/rgbif/R/occ_metadata.r | 20
rgbif-0.7.0/rgbif/R/occ_search.r | 435 ++++++++--
rgbif-0.7.0/rgbif/R/organizations.r | 17
rgbif-0.7.0/rgbif/R/parsenames.R | 2
rgbif-0.7.0/rgbif/R/zzz.r | 92 ++
rgbif-0.7.0/rgbif/README.md | 55 -
rgbif-0.7.0/rgbif/build/vignette.rds |binary
rgbif-0.7.0/rgbif/inst/assets/class_checking_occ_search.r | 2
rgbif-0.7.0/rgbif/inst/doc/rgbif_vignette.html |only
rgbif-0.7.0/rgbif/inst/doc/rgbif_vignette_oldapi.html |only
rgbif-0.7.0/rgbif/inst/singlemaplayout.html |only
rgbif-0.7.0/rgbif/inst/vign/figure/gbifmap1.png |binary
rgbif-0.7.0/rgbif/inst/vign/rgbif_vignette.Rmd | 129 ++-
rgbif-0.7.0/rgbif/inst/vign/rgbif_vignette.md | 570 +++++++++++--
rgbif-0.7.0/rgbif/man/blanktheme.Rd | 2
rgbif-0.7.0/rgbif/man/check_wkt.Rd | 15
rgbif-0.7.0/rgbif/man/commas_to_periods.Rd | 2
rgbif-0.7.0/rgbif/man/count_facet.Rd | 5
rgbif-0.7.0/rgbif/man/create_gist-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/dataset_metrics.Rd | 4
rgbif-0.7.0/rgbif/man/dataset_search.Rd | 40
rgbif-0.7.0/rgbif/man/dataset_suggest.Rd | 19
rgbif-0.7.0/rgbif/man/datasetparser.Rd | 2
rgbif-0.7.0/rgbif/man/datasets.Rd | 2
rgbif-0.7.0/rgbif/man/density_spplist-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/densitylist-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/elevation.Rd | 2
rgbif-0.7.0/rgbif/man/gbif_bbox2wkt.Rd |only
rgbif-0.7.0/rgbif/man/gbif_capwords.Rd | 2
rgbif-0.7.0/rgbif/man/gbif_photos.Rd |only
rgbif-0.7.0/rgbif/man/gbifdata-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/gbifmap.Rd | 4
rgbif-0.7.0/rgbif/man/gbifmap_dens-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/gbifmap_list-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/gbifparser.Rd | 2
rgbif-0.7.0/rgbif/man/gbifparser_verbatim.Rd | 2
rgbif-0.7.0/rgbif/man/gbifxmlToDataFrame.Rd | 2
rgbif-0.7.0/rgbif/man/get_credentials-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/gist-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/installations.Rd | 33
rgbif-0.7.0/rgbif/man/is.gbifdens-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/is.gbiflist-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/is.gbiflist_na-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/isocodes.Rd | 2
rgbif-0.7.0/rgbif/man/ldfast.Rd | 2
rgbif-0.7.0/rgbif/man/name_backbone.Rd | 2
rgbif-0.7.0/rgbif/man/name_lookup.Rd | 42 -
rgbif-0.7.0/rgbif/man/name_suggest.Rd | 16
rgbif-0.7.0/rgbif/man/name_usage.Rd | 13
rgbif-0.7.0/rgbif/man/namelkupparser.Rd | 2
rgbif-0.7.0/rgbif/man/networks.Rd | 3
rgbif-0.7.0/rgbif/man/nodes.Rd | 2
rgbif-0.7.0/rgbif/man/occ_count.Rd | 13
rgbif-0.7.0/rgbif/man/occ_get.Rd | 2
rgbif-0.7.0/rgbif/man/occ_metadata.Rd | 14
rgbif-0.7.0/rgbif/man/occ_search.Rd | 166 +++-
rgbif-0.7.0/rgbif/man/occurrencecount-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/occurrencedensity-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/occurrenceget-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/occurrencelist-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/occurrencelist_all-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/occurrencelist_many-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/organizations.Rd | 2
rgbif-0.7.0/rgbif/man/parsenames.Rd | 2
rgbif-0.7.0/rgbif/man/parseresults.Rd | 2
rgbif-0.7.0/rgbif/man/print.gbifdens-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/print.gbiflist-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/print.gbiflist_na-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/providers-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/resources-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/rgb_country_codes.Rd | 2
rgbif-0.7.0/rgbif/man/rgbif-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/rgbif.Rd | 2
rgbif-0.7.0/rgbif/man/stylegeojson-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/suggestfields.Rd | 2
rgbif-0.7.0/rgbif/man/taxoncount-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/taxonget-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/taxonsearch-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/taxrank.Rd | 2
rgbif-0.7.0/rgbif/man/togeojson-deprecated.Rd | 2
rgbif-0.7.0/rgbif/man/type_sum.Rd |only
rgbif-0.7.0/rgbif/man/typestatus.Rd | 2
rgbif-0.7.0/rgbif/tests/testthat/test-dataset_metrics.r | 2
rgbif-0.7.0/rgbif/tests/testthat/test-dataset_search.r | 5
rgbif-0.7.0/rgbif/tests/testthat/test-dataset_suggest.r | 7
rgbif-0.7.0/rgbif/tests/testthat/test-datasets.r | 3
rgbif-0.7.0/rgbif/tests/testthat/test-gbifmap.r | 5
rgbif-0.7.0/rgbif/tests/testthat/test-name_lookup.r | 2
rgbif-0.7.0/rgbif/tests/testthat/test-name_suggest.r | 4
rgbif-0.7.0/rgbif/tests/testthat/test-name_usage.r | 9
rgbif-0.7.0/rgbif/tests/testthat/test-occ_count.r | 2
rgbif-0.7.0/rgbif/tests/testthat/test-occ_get.r | 5
rgbif-0.7.0/rgbif/tests/testthat/test-occ_metadata.r | 10
rgbif-0.7.0/rgbif/tests/testthat/test-occ_search.r | 19
rgbif-0.7.0/rgbif/tests/testthat/test-organizations.r | 1
rgbif-0.7.0/rgbif/tests/testthat/test-stylegeojson.r | 6
rgbif-0.7.0/rgbif/vignettes/figure/gbifmap1.png |binary
rgbif-0.7.0/rgbif/vignettes/rgbif_vignette.Rmd | 574 +++++++++++---
128 files changed, 2397 insertions(+), 882 deletions(-)
Title: EWAS using reference-Free DNA methylation mixture deconvolution
Diff between RefFreeEWAS versions 1.2 dated 2014-03-05 and 1.3 dated 2014-07-31
Description:
Reference-free method for conducting EWAS while deconvoluting DNA methylation arising as mixtures of cell types. This method is similar to surrogate variable analysis (SVA and ISVA), except that it makes additional use of a biological mixture assumption.
Author: E. Andres Houseman, Sc.D.
Maintainer: E. Andres Houseman
DESCRIPTION | 8 ++++----
MD5 | 6 +++++-
R/PairsBootRefFreeEwasModel.R |only
man/PairsBootOneRefFreeEwasModel.Rd |only
man/PairsBootRefFreeEwasModel.Rd |only
man/bootstrapPairs.Rd |only
6 files changed, 9 insertions(+), 5 deletions(-)
Title: Least-Squares Means
Diff between lsmeans versions 2.10 dated 2014-06-24 and 2.11 dated 2014-07-31
Description: This package provides methods for obtaining least-squares means for various linear models. It can also compute contrasts or linear combinations of these least-squares means, comparisons of slopes, interaction plots, and compact letter displays.
Author: Russell V. Lenth
Maintainer: Russ Lenth
DESCRIPTION | 10 -
MD5 | 56 +++---
NAMESPACE | 2
R/KRstuff.R | 1
R/aovlist-support.R | 3
R/cld.lsm.R | 23 ++
R/helpers.R | 24 +-
R/lsm-contr.R | 16 -
R/lsmeans.R | 85 ++++++---
R/lsmip.R | 14 +
R/ref.grid.R | 200 ++++++++++++++++++-----
build/vignette.rds |binary
data/feedlot.RData |only
inst/NEWS | 19 ++
inst/doc/extending.pdf |binary
inst/doc/lsmeans-changes.pdf |binary
inst/doc/using-lsmeans.R | 225 +++++++++++++++++--------
inst/doc/using-lsmeans.pdf |binary
inst/doc/using-lsmeans.rnw | 373 +++++++++++++++++++++++++++++--------------
man/feedlot.Rd |only
man/lsmeans.Rd | 18 +-
man/lsmip.Rd | 5
man/ref.grid.Rd | 19 +-
man/ref.grid.class.Rd | 2
man/summary.Rd | 14 -
man/update.Rd | 3
tests/tests1.R | 17 +
tests/tests1.Rout.save | 70 +++++++-
vignettes/lsmeans.bib | 109 ++++++++----
vignettes/using-lsmeans.rnw | 373 +++++++++++++++++++++++++++++--------------
30 files changed, 1198 insertions(+), 483 deletions(-)
Title: Generalized Linear Autoregressive Moving Average Models
Diff between glarma versions 1.1-0 dated 2014-01-17 and 1.2-0 dated 2014-07-31
Description: This package provides functions for estimation, testing and diagnostic checking of generalized linear autoregressive moving average (GLARMA) models for discrete valued time series with regression variables. These are a class of observation driven non-linear non-Gaussian state space models. The state vector consists of a linear regression component plus an observation driven component consisting of an autoregressive-moving average (ARMA) filter of past predictive residuals. Currently three distributions (Poisson, negative binomial and binomial) can be used for the response series. Three options (Pearson, score-type and unscaled) for the residuals in the observation driven component are available. Estimation is via maximum likelihood (conditional on initializing values for the ARMA process) optimized using Fisher scoring or Newton Raphson iterative methods. Likelihood ratio and Wald tests for the observation driven component allow testing for serial dependence in generalized linear model settings. Graphical diagnostics including model fits, autocorrelation functions and probability integral transform residuals are included in the package. Several standard data sets are included in the package.
Author: William T.M. Dunsmuir
Maintainer: "William T.M. Dunsmuir"
ChangeLog | 115 +++++++++++++
DESCRIPTION | 8
MD5 | 57 +++---
R/accessors.R | 7
R/glarma.R | 315 +++++++++++++++++++------------------
R/glarmaBinomialIdentity.R | 232 +++++++++++++--------------
R/glarmaBinomialPearson.R | 244 ++++++++++++++--------------
R/glarmaBinomialScore.R | 225 +++++++++++++-------------
R/glarmaNegBinPearson.R | 300 +++++++++++++++++------------------
R/glarmaNegBinScore.R | 292 +++++++++++++++++-----------------
R/glarmaPoissonPearson.R | 284 ++++++++++++++++-----------------
R/glarmaPoissonScore.R | 288 +++++++++++++++++----------------
R/initial.R | 53 +++---
R/likTests.R | 47 ++++-
R/paramGen.R | 151 ++++++++---------
R/summary.glarma.R | 187 +++++++++++----------
TODO | 111 +++++++++++++
data/DriverDeaths.RData |only
inst/doc/glarma.R | 14 -
inst/doc/glarma.pdf |binary
inst/unitTests/runit.glarma.R | 42 ++--
inst/unitTests/runit.likTests.R | 24 +-
inst/unitTests/runit.paramGen.R | 36 ++--
inst/unitTests/runit.plot.glarma.R | 70 ++++----
man/DriverDeaths.Rd |only
man/glarma.Rd | 36 ++--
man/initial.Rd | 8
man/mySolve.Rd | 2
man/paramGen.Rd | 6
man/summary.glarma.Rd | 1
tests/offsetTests.R |only
31 files changed, 1733 insertions(+), 1422 deletions(-)
Title: Wrapper functions for FSL (FMRIB Software Library) from
Functional MRI. of the Brain (FMRIB)
Diff between fslr versions 1.0 dated 2014-06-13 and 1.1 dated 2014-07-31
Description: Wrapper functions that interface with FSL
(http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/), a powerful and commonly-used
neuroimaging software, using system commands. The goal is to be able to
interface with FSL completely in R, where you pass R nifti objects and the
function executes an FSL command and returns an R nifti object if desired.
Author: John Muschelli
Maintainer: John Muschelli
DESCRIPTION | 8 +-
MD5 | 24 ++++---
NAMESPACE | 6 +
R/fslhd.R | 160 ++++++++++++++++++++++++++++++++++++++++++++++-----
R/rescale_img.R | 4 +
build/vignette.rds |binary
man/Get-FSLDir.Rd |only
man/fslbet.Rd |only
man/fslbet.help.Rd |only
man/fslbin.Rd |only
man/fslhd.Rd | 2
man/fslmaths.Rd | 4 -
man/fslmaths.help.Rd | 1
man/fslval.Rd |only
man/fslval.help.Rd |only
man/tempimg.Rd | 2
16 files changed, 181 insertions(+), 30 deletions(-)
Title: aoristic analysis with spatial output (kml)
Diff between aoristic versions 0.4 dated 2014-03-20 and 0.5 dated 2014-07-31
Description: 'Aoristic' is one of the past tenses in Greek and represents an
uncertain occurrence time. Aoristic analysis suggested by Ratcliffe (2002)
is a method to analyze events that do not have exact times of occurrence
but have starting times and ending times. For example, a property crime
database (e.g., burglary) typically has a starting time and ending time of
the crime that could have occurred. Aoristic analysis allocates the
probability of a crime incident occurring at every hour over a 24-hour
period. The probability is aggregated over a study area to create an
aoristic graph.
Using crime incident data with lat/lon, DateTimeFrom, and
DateTimeTo, functions in this package create a total of three (3) kml
files and corresponding aoristic graphs: 1) density and contour; 2) grid
count; and 3) shapefile boundary. (see also:
https://sites.google.com/site/georgekick/software)
Author: George Kikuchi
Maintainer: George Kikuchi
aoristic-0.4/aoristic/inst/test.R |only
aoristic-0.5/aoristic/DESCRIPTION | 12 +++---
aoristic-0.5/aoristic/MD5 | 39 +++++++++----------
aoristic-0.5/aoristic/NAMESPACE | 4 ++
aoristic-0.5/aoristic/R/aoristic.all.graph.R | 8 ++--
aoristic-0.5/aoristic/R/aoristic.density.R | 37 ++++++++++++++----
aoristic-0.5/aoristic/R/aoristic.df.R | 10 ++---
aoristic-0.5/aoristic/R/aoristic.grid.R | 42 ++++++++++++++++-----
aoristic-0.5/aoristic/R/aoristic.shp.R | 48 +++++++++++++++++++-----
aoristic-0.5/aoristic/R/aoristic.spdf.R | 10 ++++-
aoristic-0.5/aoristic/demo/aoristic.R | 2 +
aoristic-0.5/aoristic/man/CouncilDistrict.Rd | 4 +-
aoristic-0.5/aoristic/man/aoristic-package.Rd | 20 +++-------
aoristic-0.5/aoristic/man/aoristic.Rd | 4 +-
aoristic-0.5/aoristic/man/aoristic.all.graph.Rd | 14 ++++---
aoristic-0.5/aoristic/man/aoristic.density.Rd | 22 +++++++----
aoristic-0.5/aoristic/man/aoristic.df.Rd | 20 +++-------
aoristic-0.5/aoristic/man/aoristic.grid.Rd | 19 +++++----
aoristic-0.5/aoristic/man/aoristic.shp.Rd | 18 ++++-----
aoristic-0.5/aoristic/man/aoristic.spdf.Rd | 21 +++-------
aoristic-0.5/aoristic/man/arlington.Rd | 4 +-
21 files changed, 214 insertions(+), 144 deletions(-)