Title: R interface to the Vowpal Wabbit
Diff between RVowpalWabbit versions 0.0.4 dated 2011-09-26 and 0.0.5 dated 2012-05-20
Description: R interface to Vowpal Wabbit fast out-of-core learning
system The Vowpal Wabbit (VW) project is a fast out-of-core
learning system sponsored by Yahoo! Research and written by
John Langford along with a number of contributors.
There are two ways to have a fast learning algorithm: (a) start with a
slow algorithm and speed it up, or (b) build an intrinsically
fast learning algorithm. This project is about approach (b),
and it has reached a state where it may be useful to others as
a platform for research and experimentation.
There are several optimization algorithms available with the baseline
being sparse gradient descent (GD) on a loss function (several
are available). The code should be easily usable. Its only
external dependence is on the Boost library, which is often
installed by default.
This R package does not include the distributed computing
implementation of the cluster/ directory of the upstream
sources. Use of the software as a network servie is also not
directly supported as the aim is a simpler direct call from R
for validation and comparison.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
ChangeLog | 24 +++++
DESCRIPTION | 8 -
MD5 | 68 +++++++--------
cleanup | 3
configure | 210 +++++++++++++++++++++++++----------------------
configure.in | 44 ++++-----
src/Makevars.in | 1
src/R_vw.cpp | 22 ++--
src/accumulate.cc | 5 -
src/active_interactor.cc | 32 +++----
src/allreduce.cc | 84 ++++++++----------
src/bfgs.cc | 56 +++++++-----
src/cache.cc | 8 +
src/comp_io.h | 7 +
src/delay_ring.cc | 1
src/gd.cc | 27 +++---
src/gd.h | 3
src/gd_mf.cc | 20 ++--
src/global_data.cc | 24 +++--
src/io.h | 8 +
src/loss_functions.cc | 10 +-
src/message_relay.cc | 1
src/multisource.cc | 24 ++---
src/network.cc | 15 +--
src/noop.cc | 1
src/parse_args.cc | 106 +++++++++++------------
src/parse_example.cc | 23 +++--
src/parse_primitives.h | 10 +-
src/parse_regressor.cc | 44 ++++-----
src/parser.cc | 61 +++++--------
src/sender.cc | 5 -
src/simple_label.cc | 8 +
src/sparse_dense.cc | 1
src/unique_sort.cc | 1
src/vw.cc | 10 +-
35 files changed, 519 insertions(+), 456 deletions(-)
Title: Fishery Stock Assessment by Catch Dynamic Models
Diff between CatDyn versions 1.0-3 dated 2011-07-25 and 1.0-4 dated 2012-05-20
Description: Using catch in biomass, fishing effort, and mean body mass
by time step, estimate stock abundance, natural mortality rate,
and fishing operational parameters. It includes methods for
plotting standard exploratory and analytical plots and to
pre-process data, five types of catch dynamics models of
increasing complexity, and two distributions for the catch
data.
Author: Ruben H. Roa Ureta
Maintainer: Ruben H. Roa Ureta
DESCRIPTION | 10
MD5 |only
R/BioFishpDay.Fk.R |only
R/CDMN0P.Lik.R | 47 +--
R/CDMN0P.Lik.gr.R | 131 +++++-----
R/CDMN0P.R | 3
R/CDMN1P.Lik.R | 59 ++--
R/CDMN1P.Lik.gr.R | 179 ++++++--------
R/CDMN1P.R | 1
R/CDMN2P.Lik.R | 69 ++---
R/CDMN2P.Lik.gr.R | 231 +++++++++---------
R/CDMN2P.R | 1
R/CDMN3P.Lik.R | 77 ++----
R/CDMN3P.Lik.gr.R | 299 +++++++++++-------------
R/CDMN3P.R | 1
R/CDMN4P.Lik.R | 85 +++---
R/CDMN4P.Lik.gr.R | 347 +++++++++++++--------------
R/CDMN4P.R | 1
R/CatDynData.R | 1
R/CatDynMod.R | 1
R/MBWpDaypSam.Fk.R |only
R/catdyn.R | 522 +++++++++++++++++++++---------------------
R/plot.CatDynData.R | 35 +-
R/plot.CatDynMod.R | 1
data/BioData.rda |only
data/CatEffData.rda |only
data/SeasonData.1990.S1.B.rda |binary
data/SeasonDates.rda |only
man/BioData.Rd |only
man/BioFishpDay.Fk.Rd |only
man/CDMN0P.Lik.Rd | 6
man/CDMN0P.Lik.gr.Rd | 8
man/CDMN0P.Rd | 22 -
man/CDMN1P.Lik.Rd | 6
man/CDMN1P.Lik.gr.Rd | 11
man/CDMN1P.Rd | 20 -
man/CDMN2P.Lik.Rd | 8
man/CDMN2P.Lik.gr.Rd | 11
man/CDMN2P.Rd | 20 -
man/CDMN3P.Lik.Rd | 6
man/CDMN3P.Lik.gr.Rd | 11
man/CDMN3P.Rd | 20 -
man/CDMN4P.Lik.Rd | 6
man/CDMN4P.Lik.gr.Rd | 9
man/CDMN4P.Rd | 20 -
man/CatDyn-package.Rd | 33 +-
man/CatEffData.Rd |only
man/MBWpDaypSam.Fk.Rd |only
man/SeasonData.1990.S1.B.Rd | 2
man/SeasonDates.Rd |only
man/catdyn.Rd | 233 +++++++-----------
man/plot.CatDynData.Rd | 5
man/plot.CatDynMod.Rd | 12
53 files changed, 1230 insertions(+), 1340 deletions(-)
Title: Utility functions to execute standard ETL operations (using
package ff) on large data.
Diff between ETLUtils versions 1.0 dated 2012-03-27 and 1.1 dated 2012-05-20
Description: Provides functions to facilitate the use of the ff package
in interaction with bigdata in SQL databases (e.g. in
Oracle/MySQL/PostgreSQL) by allowing easy importing directly
into ffdf objects using DBI and RODBC. Also contains some
basic utility functions to do fast left outer join merging
based on match and basic recoding.
Author: Jan Wijffels
Maintainer: Jan Wijffels
ETLUtils-1.0/ETLUtils/R/ETLUtils-package.R |only
ETLUtils-1.0/ETLUtils/R/ffutils.R |only
ETLUtils-1.1/ETLUtils/DESCRIPTION | 33 ++--
ETLUtils-1.1/ETLUtils/MD5 | 29 ++--
ETLUtils-1.1/ETLUtils/NAMESPACE | 5
ETLUtils-1.1/ETLUtils/NEWS | 3
ETLUtils-1.1/ETLUtils/R/ffsql.R |only
ETLUtils-1.1/ETLUtils/R/matchmerge.R | 4
ETLUtils-1.1/ETLUtils/R/pkg.R |only
ETLUtils-1.1/ETLUtils/R/utils.R | 14 +-
ETLUtils-1.1/ETLUtils/inst/smalldb.sqlite3 |binary
ETLUtils-1.1/ETLUtils/man/ETLUtils-package.Rd | 30 ++--
ETLUtils-1.1/ETLUtils/man/matchmerge.Rd | 160 ++++++++++++++++--------
ETLUtils-1.1/ETLUtils/man/naLOCFPlusone.Rd | 35 +++--
ETLUtils-1.1/ETLUtils/man/read.dbi.ffdf.Rd | 172 +++++++++++++++++---------
ETLUtils-1.1/ETLUtils/man/read.odbc.ffdf.Rd |only
ETLUtils-1.1/ETLUtils/man/recoder.Rd | 38 ++++-
ETLUtils-1.1/ETLUtils/man/renameColumns.Rd | 42 ++++--
18 files changed, 371 insertions(+), 194 deletions(-)
Title: Tools for saving, restoring and teleporting R sessions.
Diff between sessionTools versions 0.9-1 dated 2012-03-05 and 0.9-2 dated 2012-05-20
Description: This package builds on the save.session function by making
installed packages, options and search paths savable and
restorable.
Author: Matthew D. Furia
Maintainer: Matthew D. Furia
DESCRIPTION | 12 +--
MD5 | 23 ++++--
NAMESPACE | 1
R/restoreClassDefinitions.R |only
R/restoreGenerics.R |only
R/restoreObjects.R | 27 ++++++-
R/restoreS4Methods.R |only
R/restoreSession.R | 15 +++-
R/saveSession.R | 27 ++++++-
inst/tests/test_restoreClassDefinitions.R |only
inst/tests/test_restoreGenerics.R |only
inst/tests/test_restoreObjects.R | 90 +++++++++++++++++++++++-
inst/tests/test_restoreS4Methods.R |only
inst/tests/test_saveSession.R | 112 ++++++++++++++++++++++++++++++
man/restoreClassDefinitions.Rd |only
man/restoreGenerics.Rd |only
man/restoreS4Methods.Rd |only
17 files changed, 282 insertions(+), 25 deletions(-)
Title: Tools for analysing OmniLog(R) Phenotype Microarray data
Diff between opm versions 0.4-0 dated 2012-04-21 and 0.5-0 dated 2012-05-20
Description: Tools for analysing OmniLog(R) Phenotype Microarray (PM)
data as produced by the device distributed by BiOLOG Inc.,
including plotting, aggregating (estimating curve parameters),
comparing and discretizing PM data, creating phylogenetic
formats and reports for taxonomic journals, integrating
metadata, using the YAML format for the storage of data and
metadata, and batch conversion of large numbers of files.
Author: Markus Goeker, with contributions by Lea A.I. Vaas, Johannes
Sikorski, Nora Buddruhs and Anne Fiebig
Maintainer: Markus Goeker
opm-0.4-0/opm/man/normalize_plate_name.Rd |only
opm-0.5-0/opm/DESCRIPTION | 10
opm-0.5-0/opm/MD5 | 157 ++++++-----
opm-0.5-0/opm/NAMESPACE | 4
opm-0.5-0/opm/NEWS | 52 +++
opm-0.5-0/opm/R/constants.R | 1
opm-0.5-0/opm/R/helpers.R | 401 ++++++++++++++++++++----------
opm-0.5-0/opm/R/io.R | 51 +--
opm-0.5-0/opm/R/list.R | 254 ++++++++-----------
opm-0.5-0/opm/R/matrix.R | 26 -
opm-0.5-0/opm/R/numeric.R | 99 ++++---
opm-0.5-0/opm/R/opm.R | 146 ++++++++--
opm-0.5-0/opm/R/opma.R | 46 ++-
opm-0.5-0/opm/R/opms.R | 261 ++++++++++++-------
opm-0.5-0/opm/R/opmx.R | 2
opm-0.5-0/opm/R/phylo.R | 55 +---
opm-0.5-0/opm/R/wmd.R | 149 ++++++++---
opm-0.5-0/opm/inst/scripts/run_opm.R | 54 +++-
opm-0.5-0/opm/man/MOA.Rd | 8
opm-0.5-0/opm/man/OPM.Rd | 14 -
opm-0.5-0/opm/man/OPMA.Rd | 8
opm-0.5-0/opm/man/OPMS.Rd | 30 +-
opm-0.5-0/opm/man/OPMX.Rd | 8
opm-0.5-0/opm/man/WMD.Rd | 22 +
opm-0.5-0/opm/man/YAML_VIA_LIST.Rd | 8
opm-0.5-0/opm/man/aggr_settings.Rd | 6
opm-0.5-0/opm/man/aggregated.Rd | 6
opm-0.5-0/opm/man/anyDuplicated.Rd | 25 -
opm-0.5-0/opm/man/bracket.Rd | 35 +-
opm-0.5-0/opm/man/case.Rd |only
opm-0.5-0/opm/man/collect_template.Rd | 6
opm-0.5-0/opm/man/contains.Rd | 29 +-
opm-0.5-0/opm/man/csv_data.Rd | 6
opm-0.5-0/opm/man/dim.Rd | 6
opm-0.5-0/opm/man/do_aggr.Rd | 32 ++
opm-0.5-0/opm/man/duplicated.Rd | 31 +-
opm-0.5-0/opm/man/extract_columns.Rd | 6
opm-0.5-0/opm/man/filename.Rd | 6
opm-0.5-0/opm/man/find_positions.Rd | 17 -
opm-0.5-0/opm/man/find_substrate.Rd | 15 -
opm-0.5-0/opm/man/glob_to_regex.Rd | 13
opm-0.5-0/opm/man/group_by_sep.Rd | 6
opm-0.5-0/opm/man/has_aggr.Rd | 6
opm-0.5-0/opm/man/hours.Rd | 6
opm-0.5-0/opm/man/include_metadata.Rd | 6
opm-0.5-0/opm/man/infix.k.Rd | 14 -
opm-0.5-0/opm/man/infix.largek.Rd | 14 -
opm-0.5-0/opm/man/infix.largeq.Rd | 33 +-
opm-0.5-0/opm/man/infix.q.Rd | 18 +
opm-0.5-0/opm/man/insert.Rd | 3
opm-0.5-0/opm/man/is_constant.Rd | 2
opm-0.5-0/opm/man/is_uniform.Rd | 2
opm-0.5-0/opm/man/length.Rd | 6
opm-0.5-0/opm/man/map_metadata.Rd | 26 +
opm-0.5-0/opm/man/map_names.Rd | 24 -
opm-0.5-0/opm/man/map_values.Rd | 87 ++++--
opm-0.5-0/opm/man/max.Rd | 6
opm-0.5-0/opm/man/measurements.Rd | 6
opm-0.5-0/opm/man/metadata.Rd | 16 -
opm-0.5-0/opm/man/metadata.set.Rd | 109 ++++++--
opm-0.5-0/opm/man/metadata_chars.Rd | 5
opm-0.5-0/opm/man/minmax.Rd | 6
opm-0.5-0/opm/man/parse_formula_head.Rd |only
opm-0.5-0/opm/man/plate_type.Rd | 64 +++-
opm-0.5-0/opm/man/plates.Rd | 35 ++
opm-0.5-0/opm/man/position.Rd | 6
opm-0.5-0/opm/man/prepare_k.Rd |only
opm-0.5-0/opm/man/repair_na_strings.Rd | 3
opm-0.5-0/opm/man/run_kmeans.Rd | 13
opm-0.5-0/opm/man/run_native_kmeans.Rd |only
opm-0.5-0/opm/man/select.Rd | 6
opm-0.5-0/opm/man/separate.Rd | 30 +-
opm-0.5-0/opm/man/seq.Rd | 6
opm-0.5-0/opm/man/setup_time.Rd | 6
opm-0.5-0/opm/man/show.Rd |only
opm-0.5-0/opm/man/summary.Rd | 10
opm-0.5-0/opm/man/taste.Rd |only
opm-0.5-0/opm/man/thin_out.Rd | 6
opm-0.5-0/opm/man/tidy.Rd | 18 -
opm-0.5-0/opm/man/to_metadata.Rd | 5
opm-0.5-0/opm/man/well.Rd | 6
opm-0.5-0/opm/man/well_to_substrate.Rd | 12
opm-0.5-0/opm/man/wells.Rd | 6
83 files changed, 1791 insertions(+), 947 deletions(-)