Title: Generalized Partially Linear Tree-based Regression Model
Diff between GPLTR versions 0.95 dated 2014-05-27 and 1.1 dated 2014-12-19
Description: Combining a generalized linear model with an additional tree part
on the same scale. A four-step procedure is proposed to fit the model and test
the joint effect of the selected tree part while adjusting on confounding factors.
We also proposed an ensemble procedure based on the bagging to improve prediction
accuracy and computed several scores of importance for variable selection.
Author: Cyprien Mbogning
Maintainer: Cyprien Mbogning
DESCRIPTION | 15 +-
MD5 | 68 +++++----
R/Imp_Score.R |only
R/bag.aucoob.R |only
R/bagging.pltr.R | 148 ++++++++++++--------
R/best.tree.BIC.AIC.R | 5
R/best.tree.CV.R | 14 +
R/best.tree.bootstrap.R | 7
R/best.tree.permute.R | 7
R/nested.trees.R | 7
R/p.val.tree.R | 7
R/pltr.glm.R | 6
R/predict_bagg.pltr.R | 56 ++++---
R/predict_pltr.R |only
R/tree2glm.R | 3
R/tree2indicators.R | 1
build/vignette.rds |binary
inst/doc/GPLTR-manual.pdf |binary
inst/doc/intro.R | 209 ++++++++++++++++++++++++----
inst/doc/intro.Rnw | 330 ++++++++++++++++++++++++++++++++++++++-------
inst/doc/intro.pdf |binary
man/GPLTR-package.Rd | 188 +++++++++++++------------
man/VIMPBAG.Rd |only
man/bag.aucoob.Rd |only
man/bagging.pltr.Rd | 77 +++++-----
man/best.tree.BIC.AIC.Rd | 69 ++++++---
man/best.tree.CV.Rd | 41 +++--
man/best.tree.bootstrap.Rd | 27 +--
man/best.tree.permute.Rd | 40 +++--
man/nested.trees.Rd | 53 ++-----
man/p.val.tree.Rd | 51 +++---
man/pltr.glm.Rd | 44 ++++--
man/predict_bagg.pltr.Rd | 66 ++++++---
man/predict_pltr.Rd |only
man/tree2glm.Rd | 60 +++-----
man/tree2indicators.Rd | 50 ++----
vignettes/Bibliopltr.bib | 11 +
vignettes/intro.Rnw | 330 ++++++++++++++++++++++++++++++++++++++-------
38 files changed, 1382 insertions(+), 608 deletions(-)
Title: Smooth Backfitting
Diff between sBF versions 1.1 dated 2012-08-01 and 1.1.1 dated 2014-12-19
Description: Smooth Backfitting for additive models using
Nadaraya-Watson estimator
Author: A. Arcagni, L. Bagnato
Maintainer: Alberto Arcagni
DESCRIPTION | 9 +++++----
MD5 | 4 ++--
man/K.Rd | 7 -------
3 files changed, 7 insertions(+), 13 deletions(-)
Title: A Google Analytics API client for R
Diff between RGA versions 0.1.3 dated 2014-10-27 and 0.1.4 dated 2014-12-19
Description: Provides functions for accessing and retrieving data from the
Google Analytics APIs (https://developers.google.com/analytics/). Supports
OAuth 2.0 authorization. Package provides access to the Management, Core
Reporting, Multi-Channel Funnels Reporting, Real Time Reporting and
Metadata APIs. Access to all the Google Analytics accounts which the user
has access to. Auto-pagination to return more than 10,000 rows of the
results by combining multiple data requests. Also the RGA package provides
shiny app to explore the core reporting API dimensions and metrics.
Author: Artem Klevtsov [aut, cre],
Philipp Upravitelev [ctb],
Olga Shramko [ctb]
Maintainer: Artem Klevtsov
RGA-0.1.3/RGA/R/mgmt.R |only
RGA-0.1.3/RGA/man/get_accounts.Rd |only
RGA-0.1.3/RGA/man/get_goals.Rd |only
RGA-0.1.3/RGA/man/get_profiles.Rd |only
RGA-0.1.3/RGA/man/get_report.Rd |only
RGA-0.1.3/RGA/man/get_segments.Rd |only
RGA-0.1.3/RGA/man/get_webproperties.Rd |only
RGA-0.1.3/RGA/man/set_query.Rd |only
RGA-0.1.4/RGA/DESCRIPTION | 14 +--
RGA-0.1.4/RGA/MD5 | 65 ++++++++--------
RGA-0.1.4/RGA/NAMESPACE | 29 ++-----
RGA-0.1.4/RGA/R/auth.R | 18 ++--
RGA-0.1.4/RGA/R/convert.R | 62 ++++++++-------
RGA-0.1.4/RGA/R/data.R | 2
RGA-0.1.4/RGA/R/get-data.R | 123 ++----------------------------
RGA-0.1.4/RGA/R/get-mgmt.R |only
RGA-0.1.4/RGA/R/get-pages.R |only
RGA-0.1.4/RGA/R/list-mgmt.R |only
RGA-0.1.4/RGA/R/package.R | 2
RGA-0.1.4/RGA/R/query.R | 127 ++------------------------------
RGA-0.1.4/RGA/R/report.R | 118 ++++++++++++++---------------
RGA-0.1.4/RGA/R/request.R |only
RGA-0.1.4/RGA/R/shiny.R | 7 +
RGA-0.1.4/RGA/R/sysdata.rda |binary
RGA-0.1.4/RGA/R/url.R | 30 ++++---
RGA-0.1.4/RGA/R/utils.R | 22 +++++
RGA-0.1.4/RGA/R/zzz.R |only
RGA-0.1.4/RGA/README.md | 73 ++++++++++++------
RGA-0.1.4/RGA/man/RGA.Rd | 5 -
RGA-0.1.4/RGA/man/authorize.Rd | 15 ++-
RGA-0.1.4/RGA/man/dims_mets.Rd | 9 ++
RGA-0.1.4/RGA/man/ga.Rd | 5 -
RGA-0.1.4/RGA/man/get_firstdate.Rd | 14 +--
RGA-0.1.4/RGA/man/get_ga.Rd | 21 +++--
RGA-0.1.4/RGA/man/get_goal.Rd |only
RGA-0.1.4/RGA/man/get_mcf.Rd | 18 ++--
RGA-0.1.4/RGA/man/get_profile.Rd |only
RGA-0.1.4/RGA/man/get_rt.Rd | 12 +--
RGA-0.1.4/RGA/man/get_webproperty.Rd |only
RGA-0.1.4/RGA/man/list_accounts.Rd |only
RGA-0.1.4/RGA/man/list_goals.Rd |only
RGA-0.1.4/RGA/man/list_profiles.Rd |only
RGA-0.1.4/RGA/man/list_segments.Rd |only
RGA-0.1.4/RGA/man/list_webproperties.Rd |only
44 files changed, 327 insertions(+), 464 deletions(-)
Title: L1 (lasso and fused lasso) and L2 (ridge) penalized estimation
in GLMs and in the Cox model
Diff between penalized versions 0.9-42 dated 2012-11-06 and 0.9-45 dated 2014-12-19
Description: A package for fitting possibly high dimensional penalized
regression models. The penalty structure can be any combination
of an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a
positivity constraint on the regression coefficients. The
supported regression models are linear, logistic and Poisson
regression and the Cox Proportional Hazards model.
Cross-validation routines allow optimization of the tuning
parameters.
Author: Jelle Goeman, Rosa Meijer, Nimisha Chaturvedi
Maintainer: Jelle Goeman
penalized-0.9-42/penalized/changelog.txt |only
penalized-0.9-42/penalized/inst/CITATION |only
penalized-0.9-42/penalized/inst/doc/penalized.bib |only
penalized-0.9-45/penalized/ChangeLog |only
penalized-0.9-45/penalized/DESCRIPTION | 25 -
penalized-0.9-45/penalized/MD5 | 28 -
penalized-0.9-45/penalized/NAMESPACE | 2
penalized-0.9-45/penalized/R/breslow.R | 2
penalized-0.9-45/penalized/R/core.R | 518 +++++++++------------
penalized-0.9-45/penalized/R/cox.R | 2
penalized-0.9-45/penalized/R/cvl.R | 2
penalized-0.9-45/penalized/R/penfit.R | 13
penalized-0.9-45/penalized/build |only
penalized-0.9-45/penalized/inst/doc/penalized.R |only
penalized-0.9-45/penalized/inst/doc/penalized.Rnw | 35 -
penalized-0.9-45/penalized/inst/doc/penalized.pdf |binary
penalized-0.9-45/penalized/man/cvl.Rd | 26 -
penalized-0.9-45/penalized/vignettes/penalized.Rnw | 4
18 files changed, 304 insertions(+), 353 deletions(-)
Title: Interface to www.geonames.org web service
Diff between geonames versions 0.997 dated 2014-10-19 and 0.998 dated 2014-12-19
Description: Code for querying the web service at www.geonames.org
Author: Barry Rowlingson
Maintainer: Barry Rowlingson
DESCRIPTION | 6 +++---
MD5 | 4 ++--
README.md | 2 +-
3 files changed, 6 insertions(+), 6 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Diff between vardpoor versions 0.2.0.14 dated 2014-11-04 and 0.2.1 dated 2014-12-19
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, crossectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks
DESCRIPTION | 11
MD5 | 80 ++---
NAMESPACE | 2
R/domain.R | 7
R/incPercentile.R | 41 +-
R/lin.ratio.R | 4
R/linarpr.R | 75 ++---
R/linarpt.R | 40 +-
R/lingini.R | 35 +-
R/lingini2.R | 38 +-
R/lingpg.R | 35 +-
R/linpoormed.R | 44 +--
R/linqsr.R | 43 +-
R/linrmpg.R | 42 +-
R/residual_est.R | 2
R/var_srs.R | 3
R/vardchanges.R | 701 +++++++++++++++++++++---------------------------
R/vardcros.R | 185 ++++++------
R/vardom.R | 92 +++---
R/vardom_othstr.R | 64 ++--
R/vardomh.R | 86 +++--
R/variance_est.R | 24 -
R/variance_othstr.R | 28 +
R/varpoord.R | 192 ++++++-------
inst/CITATION | 6
man/incPercentile.Rd | 6
man/linarpr.Rd | 12
man/linarpt.Rd | 8
man/lingini.Rd | 8
man/lingini2.Rd | 8
man/lingpg.Rd | 12
man/linpoormed.Rd | 8
man/linqsr.Rd | 8
man/linrmpg.Rd | 8
man/vardchanges.Rd | 151 ++++------
man/vardcros.Rd | 27 +
man/vardom.Rd | 58 +--
man/vardom_othstr.Rd | 57 +--
man/vardomh.Rd | 55 +--
man/vardpoor-package.Rd | 6
man/varpoord.Rd | 68 +---
41 files changed, 1147 insertions(+), 1233 deletions(-)
Title: R-Based API for accessing the MSKCC Cancer Genomics Data Server
(CGDS).
Diff between cgdsr versions 1.1.31 dated 2014-12-12 and 1.1.32 dated 2014-12-19
Description: The package provides a basic set of R functions for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).
Author: Anders Jacobsen Skanderup
Maintainer: Anders Jacobsen Skanderup
ChangeLog | 4 ++++
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/cgdsr.R | 16 ++++++++--------
inst/doc/cgdsr.pdf |binary
5 files changed, 20 insertions(+), 16 deletions(-)
Title: Gaussian Mixture Modeling Algorithms And The Belief-based
Mixture Modeling
Diff between bgmm versions 1.6 dated 2013-11-19 and 1.7 dated 2014-12-19
Description: Two partially supervised mixture modeling methods:
soft-label and belief-based modeling are implemented.
For completeness, we equipped the package also with the
functionality of unsupervised, semi- and fully supervised
mixture modeling. The package can be applied also to selection
of the best-fitting from a set of models with different
component numbers or constraints on their structures.
For detailed introduction see:
Przemyslaw Biecek, Ewa Szczurek, Martin Vingron, Jerzy
Tiuryn (2012), The R Package bgmm: Mixture Modeling with
Uncertain Knowledge, Journal of Statistical Software.
Author: Przemyslaw Biecek \& Ewa Szczurek
Maintainer: Przemyslaw Biecek
DESCRIPTION | 18 -
MD5 | 29 -
NAMESPACE | 4
R/bgmm.e.step.r | 21 +
R/bgmm.r | 809 ++++++++++++++++++++++++-------------------------
R/get.simple.beliefs.r | 192 +++++------
R/soft.e.step.r | 97 +++--
README.md |only
demo/00Index | 2
demo/bgmm.r | 174 +++++-----
inst/CITATION | 44 +-
man/Ste12.Rd | 106 +++---
man/bgmm-package.Rd | 78 ++--
man/mModel.Rd | 266 ++++++++--------
man/miRNA.Rd | 96 ++---
man/tools.Rd | 74 ++--
16 files changed, 1023 insertions(+), 987 deletions(-)
Title: Reverse correlation image classification toolbox
Diff between rcicr versions 0.2.5 dated 2014-11-17 and 0.2.6 dated 2014-12-19
Description: Functions to generate stimuli and analyze data of reverse correlation image classification experiments.
Author: Ron Dotsch
Maintainer: Ron Dotsch
ChangeLog | 9 +++++++++
DESCRIPTION | 12 ++++++------
MD5 | 8 ++++----
R/rcicr.R | 2 ++
R/rcicr_2IFC.R | 18 +++++++++++++++++-
5 files changed, 38 insertions(+), 11 deletions(-)
Title: Another Object Orientation System
Diff between aoos versions 0.0.3 dated 2014-11-14 and 0.1.0 dated 2014-12-19
Description: Another implementation of object-orientation in R. Has reference
semantics and is build around S4.
Author: Sebastian Warnholz
Maintainer: Sebastian Warnholz
aoos-0.0.3/aoos/R/oom.R |only
aoos-0.0.3/aoos/man/oom.Rd |only
aoos-0.1.0/aoos/DESCRIPTION | 24 +++----
aoos-0.1.0/aoos/MD5 | 26 ++++---
aoos-0.1.0/aoos/NAMESPACE | 6 +
aoos-0.1.0/aoos/NEWS | 22 ++++++
aoos-0.1.0/aoos/R/aoos.R |only
aoos-0.1.0/aoos/R/defineClass.R | 60 ++++++++++++------
aoos-0.1.0/aoos/R/public-interfaces.R | 38 ++++++++++-
aoos-0.1.0/aoos/build |only
aoos-0.1.0/aoos/inst |only
aoos-0.1.0/aoos/man/aoos.Rd |only
aoos-0.1.0/aoos/man/defineClass.Rd | 42 +++++++-----
aoos-0.1.0/aoos/man/publicInterface.Rd |only
aoos-0.1.0/aoos/tests/testthat/test-basics.R | 60 ++++++++++++++----
aoos-0.1.0/aoos/tests/testthat/test-publicInterface.R | 41 +++++++++++-
aoos-0.1.0/aoos/vignettes |only
17 files changed, 241 insertions(+), 78 deletions(-)
Title: Power and Sample Size Based on Two One-sided t-Tests (TOST) for
(Bio)Equivalence Studies
Diff between PowerTOST versions 1.2-03 dated 2014-11-13 and 1.2-04 dated 2014-12-19
Description: Contains functions to calculate power and sample size for
various study designs used for bioequivalence studies.
See function known.designs() for study designs covered.
Moreover the package contains functions for power and sample size
based on 'expected' power in case of uncertain (estimated) variability.
-----
Added are functions for the power and sample size for the ratio of
two means with normally distributed data on the original scale
(based on Fieller's confidence ('fiducial') interval).
-----
Contains further functions for power and sample size calculations based on
non-inferiority t-test. This is not a TOST procedure but eventually useful
if the question of 'non-superiority' must be evaluated.
The power and sample size calculations based on non-inferiority test may
also performed via 'expected' power in case of uncertain (estimated)
variability.
-----
Contains functions power.scABEL() and sampleN.scABEL() to calculate power
and sample size for the BE decision via scaled (widened) BE acceptance
limits based on simulations.
Contains further functions power.RSABE() and sampleN.RSABE() to calculate
power and sample size for the BE decision via reference scaled ABE criterion
according to the FDA procedure based on simulations.
Contains further functions power.NTIDFDA() and sampleN.NTIDFDA() to calculate
power and sample size for the BE decision via the FDA procedure for NTID's
based on simulations.
-----
Contains functions for power analysis of a sample size plan for ABE
(pa.ABE()), scaled ABE (pa.scABE()) and scaled ABE for NTID's (pa.NTIDFDA())
analysing power if deviating from assumptions of the plan.
-----
Contains further functions for power calculations / samplesize estimation
for dose proportionality studies using the Power model.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [aut]
Maintainer: Detlew Labes
DESCRIPTION | 14 +++++++-------
MD5 | 40 +++++++++++++++++++++-------------------
NAMESPACE | 2 ++
NEWS | 11 ++++++++++-
R/BE_CI.R | 8 +++++---
R/DesignHelpers.R | 5 ++---
R/OwensQ.R | 2 +-
R/OwensQOwen.R | 7 +++++--
R/SampleSize_noninf.R | 6 +++---
R/expSampleSize.R | 20 ++++++++------------
R/expSampleSize_noninf.R | 8 +++-----
R/exppower.R | 33 ++++++++++++++++++++++++++-------
R/exppower_noninf.R | 26 ++++++++++++++++++++++----
R/helper_dp.R | 4 ++--
R/power_noninf.R | 33 +++++++++++++++++++++++++--------
R/pvalue.TOST_Benjamin.R |only
man/CI.BE.Rd | 2 +-
man/exppower.TOST.Rd | 5 ++++-
man/exppower.noninf.Rd | 5 ++++-
man/expsampleN.noninf.Rd | 2 +-
man/power.noninf.Rd | 11 +++++------
man/pvalue.TOST.Rd |only
22 files changed, 157 insertions(+), 87 deletions(-)
Title: Helsinki open data R tools
Diff between helsinki versions 0.9.20 dated 2014-06-09 and 0.9.22 dated 2014-12-19
Description: Tools for accessing various open data sources in the Helsinki
region in Finland. Current data sources include
the Real Estate Department (district maps),
the Environmental Services Authority,
Service Map API,
Linked Events API and
Helsinki Region Infoshare statistics API.
Author: Juuso Parkkinen, Leo Lahti, Joona Lehtomaki
Maintainer: Juuso Parkkinen
helsinki-0.9.20/helsinki/man/get_omakaupunki.Rd |only
helsinki-0.9.20/helsinki/vignettes/helsinki_tutorial.txt |only
helsinki-0.9.22/helsinki/DESCRIPTION | 12 +-
helsinki-0.9.22/helsinki/MD5 | 37 ++++-----
helsinki-0.9.22/helsinki/NAMESPACE | 4
helsinki-0.9.22/helsinki/R/HSY.R | 11 ++
helsinki-0.9.22/helsinki/R/demography.R | 8 +
helsinki-0.9.22/helsinki/R/economy.R | 9 +-
helsinki-0.9.22/helsinki/R/regional_stats.R | 29 ++++---
helsinki-0.9.22/helsinki/R/services.R | 53 +++----------
helsinki-0.9.22/helsinki/README.md | 1
helsinki-0.9.22/helsinki/inst/extras/omakaupunki_removed.R |only
helsinki-0.9.22/helsinki/man/aluejakokartat.Rd | 2
helsinki-0.9.22/helsinki/man/get_economic_indicators.Rd | 4
helsinki-0.9.22/helsinki/man/get_hri_stats.Rd | 4
helsinki-0.9.22/helsinki/man/get_hsy.Rd | 4
helsinki-0.9.22/helsinki/man/get_linkedevents.Rd | 4
helsinki-0.9.22/helsinki/man/get_population_projection.Rd | 4
helsinki-0.9.22/helsinki/man/get_servicemap.Rd | 4
helsinki-0.9.22/helsinki/man/helsinki-package.Rd | 2
helsinki-0.9.22/helsinki/vignettes/todo-datasets.md | 4
21 files changed, 102 insertions(+), 94 deletions(-)
Title: Zebra-Striped Tables in LaTeX and HTML Formats
Diff between ztable versions 0.1.0 dated 2014-12-15 and 0.1.1 dated 2014-12-19
Description: Makes zebra-striped tables (tables with alternating row colors)
in LaTeX and HTML formats easily from a data.frame, matrix, lm, aov, anova,
glm or coxph objects.
Author: "Keon-Woong Moon" [aut, cre]
Maintainer: "Keon-Woong Moon"
ztable-0.1.0/ztable/vignettes/Untitled.Rmd |only
ztable-0.1.0/ztable/vignettes/ztableIntroduction.pdf |only
ztable-0.1.1/ztable/DESCRIPTION | 6
ztable-0.1.1/ztable/MD5 | 34 -
ztable-0.1.1/ztable/NEWS | 13
ztable-0.1.1/ztable/R/parallelTables.R |only
ztable-0.1.1/ztable/R/print.ztable.html.R | 3
ztable-0.1.1/ztable/R/ztable.R | 118 +++-
ztable-0.1.1/ztable/R/ztable1.R | 52 +-
ztable-0.1.1/ztable/R/zzz.R | 6
ztable-0.1.1/ztable/inst/doc/ztable.R | 19
ztable-0.1.1/ztable/inst/doc/ztable.Rmd | 30 -
ztable-0.1.1/ztable/inst/doc/ztable.html | 494 ++++++++++++++-----
ztable-0.1.1/ztable/man/parallelTables.Rd |only
ztable-0.1.1/ztable/man/parallelTablesHTML.Rd |only
ztable-0.1.1/ztable/man/parallelTablesLatex.Rd |only
ztable-0.1.1/ztable/man/print_ztable.Rd | 2
ztable-0.1.1/ztable/man/ztable.Rd | 28 -
ztable-0.1.1/ztable/man/ztable_sub.Rd | 34 +
ztable-0.1.1/ztable/vignettes/figures/ztable2.png |only
ztable-0.1.1/ztable/vignettes/figures/ztable3.png |only
ztable-0.1.1/ztable/vignettes/ztable.Rmd | 30 -
22 files changed, 643 insertions(+), 226 deletions(-)
Title: Taxonomic Information from Around the Web
Diff between taxize versions 0.4.0 dated 2014-09-09 and 0.5.2 dated 2014-12-19
Description: Taxonomic information from around the web. This package
interacts with a suite of web APIs for taxonomic tasks, such
as verifying species names, getting taxonomic hierarchies,
and verifying name spelling.
Author: Scott Chamberlain [aut, cre],
Eduard Szoecs [aut],
Zachary Foster [aut],
Carl Boettiger [aut],
Karthik Ram [aut],
Ignasi Bartomeus [aut],
John Baumgartner [aut]
Maintainer: Scott Chamberlain
taxize-0.4.0/taxize/R/deprecated.R |only
taxize-0.4.0/taxize/R/eol_ping.R |only
taxize-0.4.0/taxize/R/itis_ping.R |only
taxize-0.4.0/taxize/R/phylomatic_tree2.R |only
taxize-0.4.0/taxize/R/startup.R |only
taxize-0.4.0/taxize/inst/vign/cache/taxname_7297fd0eac6d20cb0c418a18b1be6438.RData |only
taxize-0.4.0/taxize/inst/vign/cache/taxname_7297fd0eac6d20cb0c418a18b1be6438.rdb |only
taxize-0.4.0/taxize/inst/vign/cache/taxname_7297fd0eac6d20cb0c418a18b1be6438.rdx |only
taxize-0.4.0/taxize/man/col_classification-deprecated.Rd |only
taxize-0.4.0/taxize/man/eol_hierarchy-deprecated.Rd |only
taxize-0.4.0/taxize/man/eol_invasive.Rd |only
taxize-0.4.0/taxize/man/eol_ping.Rd |only
taxize-0.4.0/taxize/man/gisd_isinvasive.Rd |only
taxize-0.4.0/taxize/man/itis_ping.Rd |only
taxize-0.4.0/taxize/man/ncbi_getbyid.Rd |only
taxize-0.4.0/taxize/man/ncbi_getbyname.Rd |only
taxize-0.4.0/taxize/man/ncbi_search.Rd |only
taxize-0.4.0/taxize/man/phylomatic_tree.Rd |only
taxize-0.4.0/taxize/man/tp_classification-deprecated.Rd |only
taxize-0.4.0/taxize/man/tpl_search-deprecated.Rd |only
taxize-0.4.0/taxize/tests/testthat/test-tpl_search.R |only
taxize-0.4.0/taxize/tests/testthat/test-ubio_classification.R |only
taxize-0.4.0/taxize/tests/testthat/test-ubio_id.R |only
taxize-0.4.0/taxize/tests/testthat/test-ubio_namebank.R |only
taxize-0.4.0/taxize/tests/testthat/test-ubio_search.R |only
taxize-0.4.0/taxize/tests/testthat/test-ubio_synonyms.R |only
taxize-0.5.2/taxize/DESCRIPTION | 16
taxize-0.5.2/taxize/MD5 | 600 ++--
taxize-0.5.2/taxize/NAMESPACE | 111
taxize-0.5.2/taxize/NEWS | 50
taxize-0.5.2/taxize/R/apg_lookup.R | 11
taxize-0.5.2/taxize/R/bold_search.R | 25
taxize-0.5.2/taxize/R/children.R | 77
taxize-0.5.2/taxize/R/class2tree.R | 46
taxize-0.5.2/taxize/R/classification.R | 430 +-
taxize-0.5.2/taxize/R/col_children.R | 58
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taxize-0.5.2/taxize/R/genbank2uid.R |only
taxize-0.5.2/taxize/R/get_boldid.R | 152 -
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taxize-0.5.2/taxize/R/get_eolid.R | 210 +
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taxize-0.5.2/taxize/R/get_nbnid.R |only
taxize-0.5.2/taxize/R/get_tpsid.R | 166 -
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taxize-0.5.2/taxize/R/get_uid.R | 186 -
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taxize-0.5.2/taxize/R/itis-api.R |only
taxize-0.5.2/taxize/R/itis.R | 1477 +++-------
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taxize-0.5.2/taxize/R/itis_downstream.R | 80
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taxize-0.5.2/taxize/R/phylomatic_tree.R | 90
taxize-0.5.2/taxize/R/ping.R |only
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taxize-0.5.2/taxize/R/tax_name.R | 161 -
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taxize-0.5.2/taxize/R/tpl_families.r | 16
taxize-0.5.2/taxize/R/tpl_get.r | 34
taxize-0.5.2/taxize/R/tpl_search.r | 8
taxize-0.5.2/taxize/R/ubio_classification.R | 32
taxize-0.5.2/taxize/R/ubio_classification_search.R | 22
taxize-0.5.2/taxize/R/ubio_id.R | 36
taxize-0.5.2/taxize/R/ubio_search.R | 18
taxize-0.5.2/taxize/R/ubio_synonyms.R | 12
taxize-0.5.2/taxize/R/upstream.R |only
taxize-0.5.2/taxize/R/vascan_search.r | 20
taxize-0.5.2/taxize/R/zzz.R | 86
taxize-0.5.2/taxize/README.md | 519 ++-
taxize-0.5.2/taxize/build/vignette.rds |binary
taxize-0.5.2/taxize/inst/doc/taxize_infotable.html | 97
taxize-0.5.2/taxize/inst/doc/taxize_vignette.Rmd | 622 +++-
taxize-0.5.2/taxize/inst/doc/taxize_vignette.html | 688 +++-
taxize-0.5.2/taxize/inst/ignore/aou_notes.R |only
taxize-0.5.2/taxize/inst/ignore/phylomatic_tree2.R |only
taxize-0.5.2/taxize/inst/ignore/tests |only
taxize-0.5.2/taxize/inst/vign/cache/taxname_f6bfd7efb6327a4d98fe2ce6978a484a.RData |only
taxize-0.5.2/taxize/inst/vign/cache/taxname_f6bfd7efb6327a4d98fe2ce6978a484a.rdb |only
taxize-0.5.2/taxize/inst/vign/cache/taxname_f6bfd7efb6327a4d98fe2ce6978a484a.rdx |only
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taxize-0.5.2/taxize/inst/vign/taxize_vignette.md | 622 +++-
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taxize-0.5.2/taxize/man/bold_search.Rd | 25
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taxize-0.5.2/taxize/man/class2tree.Rd | 5
taxize-0.5.2/taxize/man/classification.Rd | 109
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taxize-0.5.2/taxize/man/col_classification-defunct.Rd |only
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taxize-0.5.2/taxize/man/gbif_name_usage.Rd | 33
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taxize-0.5.2/taxize/man/genbank2uid.Rd |only
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taxize-0.5.2/taxize/man/get_eolid.Rd | 75
taxize-0.5.2/taxize/man/get_gbifid.Rd | 77
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taxize-0.5.2/taxize/man/get_uid.Rd | 82
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taxize-0.5.2/taxize/man/getcommonnamesfromtsn.Rd | 14
taxize-0.5.2/taxize/man/getcoremetadatafromtsn.Rd | 17
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taxize-0.5.2/taxize/man/getfullhierarchyfromtsn.Rd | 19
taxize-0.5.2/taxize/man/getfullrecordfromlsid.Rd | 19
taxize-0.5.2/taxize/man/getfullrecordfromtsn.Rd | 22
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taxize-0.5.2/taxize/man/getjurisdictionaloriginfromtsn.Rd | 17
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taxize-0.5.2/taxize/man/gisd_invasive-deprecated.Rd |only
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taxize-0.5.2/taxize/man/itis-api.Rd |only
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taxize-0.5.2/taxize/man/nbn_classifcation.Rd |only
taxize-0.5.2/taxize/man/nbn_search.Rd |only
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taxize-0.5.2/taxize/man/searchbycommonnameendswith.Rd | 17
taxize-0.5.2/taxize/man/searchbyscientificname.Rd | 19
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taxize-0.5.2/taxize/man/status_codes.Rd |only
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taxize-0.5.2/taxize/man/tax_name.Rd | 22
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taxize-0.5.2/taxize/man/tp_classification-defunct.Rd |only
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taxize-0.5.2/taxize/man/tp_synonyms.Rd | 5
taxize-0.5.2/taxize/man/tpl_families.Rd | 5
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taxize-0.5.2/taxize/man/tpl_search-defunct.Rd |only
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taxize-0.5.2/taxize/man/ubio_classification_search.Rd | 5
taxize-0.5.2/taxize/man/ubio_id.Rd | 5
taxize-0.5.2/taxize/man/ubio_search.Rd | 5
taxize-0.5.2/taxize/man/ubio_synonyms.Rd | 5
taxize-0.5.2/taxize/man/upstream.Rd |only
taxize-0.5.2/taxize/man/vascan_search.Rd | 5
taxize-0.5.2/taxize/tests/testthat/test-classification.R | 67
taxize-0.5.2/taxize/tests/testthat/test-col_children.R | 20
taxize-0.5.2/taxize/tests/testthat/test-col_downstream.R | 24
taxize-0.5.2/taxize/tests/testthat/test-comm2sci.R | 8
taxize-0.5.2/taxize/tests/testthat/test-eol_dataobjects.R | 6
taxize-0.5.2/taxize/tests/testthat/test-eol_invasive.R | 4
taxize-0.5.2/taxize/tests/testthat/test-eol_ping.R | 8
taxize-0.5.2/taxize/tests/testthat/test-eol_search.R | 6
taxize-0.5.2/taxize/tests/testthat/test-get_boldid.R | 8
taxize-0.5.2/taxize/tests/testthat/test-get_ids.R | 12
taxize-0.5.2/taxize/tests/testthat/test-get_tpsid.R | 8
taxize-0.5.2/taxize/tests/testthat/test-gisd_isinvasive.R | 2
taxize-0.5.2/taxize/tests/testthat/test-itis.R | 4
taxize-0.5.2/taxize/tests/testthat/test-itis_getrecord.R | 5
taxize-0.5.2/taxize/tests/testthat/test-itis_hierarchy.R | 5
taxize-0.5.2/taxize/tests/testthat/test-itis_kingdomnames.R | 7
taxize-0.5.2/taxize/tests/testthat/test-itis_lsid.R | 4
taxize-0.5.2/taxize/tests/testthat/test-itis_native.R | 5
taxize-0.5.2/taxize/tests/testthat/test-itis_phymat_format.R | 4
taxize-0.5.2/taxize/tests/testthat/test-itis_ping.R | 9
taxize-0.5.2/taxize/tests/testthat/test-itis_refs.R | 4
taxize-0.5.2/taxize/tests/testthat/test-ncbi_getbyname.R | 9
taxize-0.5.2/taxize/tests/testthat/test-ncbi_search.R | 4
taxize-0.5.2/taxize/tests/testthat/test-sci2comm.R | 6
taxize-0.5.2/taxize/tests/testthat/test-tax_agg.R | 11
taxize-0.5.2/taxize/tests/testthat/test-tax_name.R | 40
taxize-0.5.2/taxize/tests/testthat/test-tp_accnames.R | 4
taxize-0.5.2/taxize/tests/testthat/test-tp_summary.R | 4
taxize-0.5.2/taxize/tests/testthat/test-vascan_search.r | 12
taxize-0.5.2/taxize/vignettes/taxize_vignette.Rmd | 622 +++-
333 files changed, 7772 insertions(+), 4739 deletions(-)
Title: stream - Interface to MOA Algorithms
Diff between streamMOA versions 0.1-1 dated 2014-06-17 and 1.0-0 dated 2014-12-19
Description: This package provides an interface to algorithms implemented in the MOA (Massive Online Analysis) framework for data stream mining.
Author: Michael Hahsler [aut, cre, cph],
Matthew Bolanos [aut, cph],
John Forrest [aut, cph]
Maintainer: Michael Hahsler
DESCRIPTION | 10 -
MD5 | 35 +++--
NAMESPACE | 2
R/DSC_CluStream.R | 37 ++----
R/DSC_ClusTree.R | 31 ++---
R/DSC_DenStream.R | 29 ++--
R/DSC_MOA.R | 50 ++++----
R/DSD_MOA.R | 23 +--
build/vignette.rds |binary
inst/NEWS | 3
inst/doc/streamMOA.R | 145 +++++++++---------------
inst/doc/streamMOA.Rnw | 216 +++++++-----------------------------
inst/doc/streamMOA.pdf |binary
java |only
man/DSC_CluStream.Rd | 26 ++--
man/DSC_ClusTree.Rd | 26 ++--
man/DSC_DenStream.Rd | 18 +--
man/DSD_RandomRBFGeneratorEvents.Rd | 5
vignettes/streamMOA.Rnw | 216 +++++++-----------------------------
19 files changed, 301 insertions(+), 571 deletions(-)
Title: Bayesian Modeling and Analysis of Spatially Correlated Survival
Data
Diff between spBayesSurv versions 1.0.1 dated 2014-10-25 and 1.0.2 dated 2014-12-19
Description: This package provides several Bayesian survival models for spatial/non-spatial survival data: marginal Bayesian Nonparametric models, marginal Bayesian proportional hazards models, and generalized accelerated failure time frailty models.
Author: Haiming Zhou
Maintainer: Haiming Zhou
DESCRIPTION | 6
MD5 | 36 +-
R/anovaDDP.R | 281 +++++++++--------
R/spCopulaDDP.R | 490 +++++++++++++++---------------
man/anovaDDP.Rd | 35 +-
man/spBayesSurv-package.Rd | 2
man/spCopulaDDP.Rd | 664 ++++++++++++++++++++---------------------
src/spSurv_Coxph_tools.cpp | 9
src/spSurv_DDP_tools.cpp | 173 +++++++++-
src/spSurv_DDP_tools.h | 14
src/spSurv_anovaDDP.cpp | 50 ++-
src/spSurv_common.cpp | 174 +++++++---
src/spSurv_common.h | 7
src/spSurv_frailtyLDTFP.cpp | 3
src/spSurv_indeptCoxph.cpp | 10
src/spSurv_nonfrailtyLDTFP.cpp | 3
src/spSurv_spCopulaCoxph.cpp | 6
src/spSurv_spCopulaDDP.cpp | 124 +++++--
src/spSurv_spCopulaDDP.h | 4
19 files changed, 1211 insertions(+), 880 deletions(-)
Title: Provides access to databases through the JDBC interface
Diff between RJDBC versions 0.2-4 dated 2014-06-26 and 0.2-5 dated 2014-12-19
Description: RJDBC is an implementation of R's DBI interface using JDBC as a back-end. This allows R to connect to any DBMS that has a JDBC driver.
Author: Simon Urbanek
Maintainer: Simon Urbanek
DESCRIPTION | 6 +++---
MD5 | 12 ++++++------
NEWS | 15 ++++++++++++++-
R/class.R | 12 +++++++-----
inst/java/RJDBC.jar |binary
java-src/JDBCResultPull.java | 11 +++++++++--
man/JDBCResult-methods.Rd | 9 +++++++++
7 files changed, 48 insertions(+), 17 deletions(-)
Title: Convert R Graphics to Flash Animations
Diff between R2SWF versions 0.8-1 dated 2014-12-10 and 0.8-2 dated 2014-12-19
Description: This package uses the Ming library
(http://www.libming.org/) to create Flash animations.
Users can either use the SWF device swf() to generate SWF file
directly through plotting functions like plot() and lines(),
or convert images of other formats (SVG, PNG, JPEG) into SWF.
Author: Yixuan Qiu, Yihui Xie, Cameron Bracken and authors of included
software. See file AUTHORS for details.
Maintainer: Yixuan Qiu
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NEWS | 12 +++++++++++-
src/libming/shape_util.c | 2 +-
4 files changed, 19 insertions(+), 9 deletions(-)
Title: Local Polynomial Estimator in Measurement Error Models
Diff between lpme versions 1.0.0 dated 2014-11-05 and 1.0.1 dated 2014-12-19
Description: Two local polynomial estimators for solving the errors-in-variables problem: one is in Delaigle, Fan, and Carroll (2009), and one is in Huang and Zhou (2014+). The SIMEX bandwidth selection method is also provided for both estimators.
Author: Haiming Zhou
Maintainer: Haiming Zhou
DESCRIPTION | 6 +++---
MD5 | 4 ++--
src/lpme_common.cpp | 4 ++--
3 files changed, 7 insertions(+), 7 deletions(-)
Title: A Unified Framework for Input-Output Operations in R
Diff between io versions 0.2 dated 2014-12-11 and 0.2.1 dated 2014-12-19
Description: One function to read files. One function to write files. One
function to direct plots to screen or file. Automatic file format inference
and directory structure creation.
Author: David J. H. Shih
Maintainer: David J. H. Shih
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
R/hdf5.R | 6 ++++--
R/internal.R | 8 ++++++++
R/json.R | 4 ++--
R/xml.R | 6 ++++--
R/yaml.R | 4 ++--
tests/testthat/helper.R | 11 ++++++++++-
8 files changed, 41 insertions(+), 20 deletions(-)
Title: Binary Classifier Interpretation Functions
Diff between interpretR versions 0.1.0 dated 2014-11-21 and 0.2.0 dated 2014-12-19
Description: Compute permutation- based performance measures and create
partial dependence plots for binary (cross-validated) classification models.
Currently only binary classification models estimated with the packages
randomForest and ada are supported.
Author: Michel Ballings and Dirk Van den Poel
Maintainer: Michel Ballings
DESCRIPTION | 19 +++---
MD5 | 14 ++--
NAMESPACE | 2
R/parDepPlot.R | 131 +++++++++++++++++++++++++++++++++++++++++-----
R/variableImportance.R |only
inst/NEWS | 9 ++-
man/interpretR-package.Rd | 10 +--
man/parDepPlot.Rd | 32 ++++++++---
man/variableImportance.Rd |only
9 files changed, 173 insertions(+), 44 deletions(-)
Title: High-dimensional Kernel Density Estimation and Geometry
Operations
Diff between hypervolume versions 1.1 dated 2014-12-04 and 1.1.1 dated 2014-12-19
Description: Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and negative feature detection. Uses stochastic geometry approach to high-dimensional kernel density estimation. Builds n-dimensional convex hulls (polytopes). Can measure the n-dimensional ecological hypervolume and perform species distribution modeling.
Author: Benjamin Blonder
Maintainer: Benjamin Blonder
DESCRIPTION | 14 +++++++-------
MD5 | 6 +++---
demo/finch.R | 4 ++--
demo/quercus.R | 15 ++++++---------
4 files changed, 18 insertions(+), 21 deletions(-)
Title: Graph Estimation Based on Birth-Death MCMC Approach
Diff between BDgraph versions 2.13 dated 2014-11-17 and 2.14 dated 2014-12-19
Description: This package provides a Bayesian methodology for structure learning in undirected graphical models. Our Bayesian methodology is based on birth-death Markov chain Monte Carlo (BDMCMC) algorithm which is the main function with the name 'bdgraph'. The main target of this package is high-dimensional data analysis wherein usually p >> n. The computation is memory-optimized using the sparse matrix output.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi
BDgraph-2.13/BDgraph/R/BDgraph.R |only
BDgraph-2.13/BDgraph/R/bdgraph_select.R |only
BDgraph-2.13/BDgraph/R/bdgraph_sim.R |only
BDgraph-2.13/BDgraph/R/roc.R |only
BDgraph-2.14/BDgraph/DESCRIPTION | 8 -
BDgraph-2.14/BDgraph/MD5 | 57 ++++++-----
BDgraph-2.14/BDgraph/NAMESPACE | 5 +
BDgraph-2.14/BDgraph/R/I.g.R |only
BDgraph-2.14/BDgraph/R/bdgraph.R |only
BDgraph-2.14/BDgraph/R/bdgraph.npn.R |only
BDgraph-2.14/BDgraph/R/bdgraph.sim.R |only
BDgraph-2.14/BDgraph/R/compare.R |only
BDgraph-2.14/BDgraph/R/phat.R |only
BDgraph-2.14/BDgraph/R/plotcoda.R |only
BDgraph-2.14/BDgraph/R/plotroc.R |only
BDgraph-2.14/BDgraph/R/prob.R |only
BDgraph-2.14/BDgraph/R/rgwish.R | 136 ++--------------------------
BDgraph-2.14/BDgraph/R/rwish.R |only
BDgraph-2.14/BDgraph/R/select.R |only
BDgraph-2.14/BDgraph/R/traceplot.R |only
BDgraph-2.14/BDgraph/man/BDgraph-package.Rd | 3
BDgraph-2.14/BDgraph/man/bdgraph.Rd | 126 +++++++++++++------------
BDgraph-2.14/BDgraph/man/bdgraph.sim.Rd | 22 ++--
BDgraph-2.14/BDgraph/man/compare.Rd | 30 +++---
BDgraph-2.14/BDgraph/man/phat.Rd | 14 +-
BDgraph-2.14/BDgraph/man/plot.bdgraph.Rd | 18 +--
BDgraph-2.14/BDgraph/man/plot.simulate.Rd | 10 +-
BDgraph-2.14/BDgraph/man/plotcoda.Rd | 28 ++---
BDgraph-2.14/BDgraph/man/plotroc.Rd | 20 ++--
BDgraph-2.14/BDgraph/man/print.bdgraph.Rd | 18 +--
BDgraph-2.14/BDgraph/man/print.simulate.Rd | 10 +-
BDgraph-2.14/BDgraph/man/prob.Rd | 22 ++--
BDgraph-2.14/BDgraph/man/rgwish.Rd | 16 +--
BDgraph-2.14/BDgraph/man/rwish.Rd |only
BDgraph-2.14/BDgraph/man/select.Rd | 20 ++--
BDgraph-2.14/BDgraph/man/summary.bdgraph.Rd | 18 +--
BDgraph-2.14/BDgraph/man/traceplot.Rd | 20 ++--
BDgraph-2.14/BDgraph/src/bdmcmc.cpp | 8 -
38 files changed, 260 insertions(+), 349 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-10 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-09-12 0.9.0
2014-08-27 0.8.9
2013-12-03 0.8.2
2013-11-19 0.8.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-09-24 0.2.2
2014-08-13 0.1.1