Title: Calculating Concentration Risk under Solvency II
Description: Methods for determining spatial risk, in particular calculating the maximum value of insured fire risk policies of all buildings that are partly or fully located within circle of a radius of 200m.
Author: Martin Haringa
Maintainer: Martin Haringa <mtharinga@gmail.com>
Diff between spatialrisk versions 0.6.2 dated 2019-07-29 and 0.6.3 dated 2019-10-18
DESCRIPTION | 8 +++--- MD5 | 56 ++++++++++++++++++++++++---------------------- NAMESPACE | 2 + NEWS.md | 4 +++ R/choropleth.R |only R/concentration.R | 4 +-- R/map_ggplot2.R | 2 - R/map_tmap.R | 46 ++++--------------------------------- R/nl_gemeente.R | 28 +++++++++++++++++------ R/nlchoropleth.R | 56 ++-------------------------------------------- R/points_to_polygon.R |only data/nl_corop.rda |binary data/nl_gemeente.rda |binary data/nl_postcode1.rda |binary data/nl_postcode2.rda |binary data/nl_postcode3.rda |binary data/nl_postcode4.rda |binary data/nl_provincie.rda |binary man/choropleth.Rd |only man/choropleth_ggplot2.Rd | 2 - man/choropleth_sf.Rd | 9 ------- man/choropleth_tmap.Rd | 9 +------ man/concentration.Rd | 4 +-- man/nl_corop.Rd | 4 ++- man/nl_gemeente.Rd | 4 ++- man/nl_postcode1.Rd | 4 ++- man/nl_postcode2.Rd | 4 ++- man/nl_postcode3.Rd | 4 ++- man/nl_postcode4.Rd | 4 ++- man/nl_provincie.Rd | 4 ++- man/points_to_polygon.Rd |only 31 files changed, 100 insertions(+), 158 deletions(-)
Title: Integrative Analysis of Omics Data in Terms of Network,
Evolution and Ontology
Description: The focus of the dnet by Fang and Gough (2014) <doi:10.1186/s13073-014-0064-8> is to make sense of omics data (such as gene expression and mutations) from different angles including: integration with molecular networks, enrichments using ontologies, and relevance to gene evolutionary ages. Integration is achieved to identify a gene subnetwork from the whole gene network whose nodes/genes are labelled with informative data (such as the significant levels of differential expression or survival risks). To help make sense of identified gene networks, enrichment analysis is also supported using a wide variety of pre-compiled ontologies and phylostratific gene age information in major organisms including: human, mouse, rat, chicken, C.elegans, fruit fly, zebrafish and arabidopsis. Add-on functionalities are supports for calculating semantic similarity between ontology terms (and between genes) and for calculating network affinity based on random walk; both can be done via high-performance parallel computing.
Author: Hai Fang and Julian Gough
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Diff between dnet versions 1.1.4 dated 2018-08-10 and 1.1.5 dated 2019-10-18
DESCRIPTION | 8 ++--- MD5 | 50 +++++++++++++++++----------------- R/dNetPipeline.r | 3 +- data/TCGA_mutations.RData |binary data/ig.HPPA.RData |binary data/org.Hs.egHPPA.RData |binary man/dContrast.Rd | 3 -- man/dEnricher.Rd | 28 ++++++++----------- man/dEnricherView.Rd | 4 +- man/dGSEA.Rd | 18 +++++------- man/dGSEAwrite.Rd | 6 ++-- man/dNetInduce.Rd | 4 +- man/dNetPipeline.Rd | 7 +++- man/dNetReorder.Rd | 15 ++++------ man/dPvalAggregate.Rd | 4 +- man/dRDataLoader.Rd | 67 +++++++++++++++++++--------------------------- man/dRWR.Rd | 5 ++- man/dRWRpipeline.Rd | 4 +- man/dSVDsignif.Rd | 8 ++--- man/visBoxplotAdv.Rd | 16 +++++----- man/visNet.Rd | 5 +-- man/visNetAnimate.Rd | 10 +++--- man/visNetArc.Rd | 4 +- man/visNetCircle.Rd | 14 ++++----- man/visNetMul.Rd | 10 +++--- man/visNetReorder.Rd | 10 +++--- 26 files changed, 144 insertions(+), 159 deletions(-)
Title: Extension of `data.frame`
Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.
Author: Matt Dowle [aut, cre],
Arun Srinivasan [aut],
Jan Gorecki [ctb],
Michael Chirico [ctb],
Pasha Stetsenko [ctb],
Tom Short [ctb],
Steve Lianoglou [ctb],
Eduard Antonyan [ctb],
Markus Bonsch [ctb],
Hugh Parsonage [ctb],
Scott Ritchie [ctb],
Kun Ren [ctb],
Xianying Tan [ctb],
Rick Saporta [ctb],
Otto Seiskari [ctb],
Xianghui Dong [ctb],
Michel Lang [ctb],
Watal Iwasaki [ctb],
Seth Wenchel [ctb],
Karl Broman [ctb],
Tobias Schmidt [ctb],
David Arenburg [ctb],
Ethan Smith [ctb],
Francois Cocquemas [ctb],
Matthieu Gomez [ctb],
Philippe Chataignon [ctb],
Declan Groves [ctb],
Daniel Possenriede [ctb],
Felipe Parages [ctb],
Denes Toth [ctb],
Mus Yaramaz-David [ctb],
Ayappan Perumal [ctb],
James Sams [ctb],
Martin Morgan [ctb],
Michael Quinn [ctb],
@javrucebo [ctb],
@marc-outins [ctb],
Roy Storey [ctb],
Manish Saraswat [ctb],
Morgan Jacob [ctb],
Michael Schubmehl [ctb]
Maintainer: Matt Dowle <mattjdowle@gmail.com>
Diff between data.table versions 1.12.4 dated 2019-10-03 and 1.12.6 dated 2019-10-18
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Title: Bayesian Fertility Projection
Description: Making probabilistic projections of total fertility rate for all countries of the world, using a Bayesian hierarchical model.
Author: Hana Sevcikova (hanas@uw.edu), Leontine Alkema (alkema@nus.edu.sg), Adrian Raftery (raftery@uw.edu), Bailey Fosdick (bfosdick@uw.edu), Patrick Gerland (gerland@un.org)
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between bayesTFR versions 6.3-1 dated 2019-06-11 and 6.4-0 dated 2019-10-18
ChangeLog | 11 DESCRIPTION | 18 LICENSE |only MD5 | 1809 +++++----- NAMESPACE | 2 R/mcmc_ini.R | 4 R/plot_functions.R | 8 R/predict_tfr.R | 52 R/run_mcmc.R | 4 inst/ex-data/bayesTFR.output/bayesTFR.mcmc.meta.rda |binary inst/ex-data/bayesTFR.output/mc1/S_sd.txt.bz2 |binary inst/ex-data/bayesTFR.output/mc1/Triangle4.txt.bz2 |binary inst/ex-data/bayesTFR.output/mc1/Triangle_c4_country100.txt.bz2 |binary inst/ex-data/bayesTFR.output/mc1/Triangle_c4_country104.txt.bz2 |binary inst/ex-data/bayesTFR.output/mc1/Triangle_c4_country108.txt.bz2 |binary inst/ex-data/bayesTFR.output/mc1/Triangle_c4_country112.txt.bz2 |binary inst/ex-data/bayesTFR.output/mc1/Triangle_c4_country116.txt.bz2 |binary inst/ex-data/bayesTFR.output/mc1/Triangle_c4_country12.txt.bz2 |binary inst/ex-data/bayesTFR.output/mc1/Triangle_c4_country120.txt.bz2 |binary inst/ex-data/bayesTFR.output/mc1/Triangle_c4_country124.txt.bz2 |binary inst/ex-data/bayesTFR.output/mc1/Triangle_c4_country132.txt.bz2 |binary 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Title: 3D Brain Visualization
Description: In neuroscience, 'AFNI/SUMA' is a great tool to visualize 3D brain.
However, it takes efforts to interact and share the viewer to others. In
addition, 'AFNI/SUMA' doesn't support Windows platform. In the 'EEG/iEEG'
field, it's hard to have multiple cortical electrodes mapped to a template
brain for group analysis. Therefore this package is written aimed at
providing a fast, stable, interactive and easy to share tool based on 'Three.js',
a 'WebGL' engine to render 3D objects in the web browser such that we can
display brain surfaces on webpage interactively. This package translates R
objects to JavaScript objects via 'JSON' format, and provides 'R-Shiny' interface
to manipulate geometries interactively. The visualizations can also serve as
standalone widgets that can be easily shared across different platforms.
Along with 'rave', another package developed by Beauchamp's lab at Baylor
College Medicine, this package provides solutions to easily map surface
electrodes from multiple subjects to one template 141 brain.
Author: Zhengjia Wang [aut, cre, cph],
John Magnotti [aut],
Brian Metzger [aut],
Elizabeth Nesbitt [res],
Michael Beauchamp [aut, dtc, fnd]
Maintainer: Zhengjia Wang <zhengjia.wang@rice.edu>
Diff between threeBrain versions 0.1.3 dated 2019-09-10 and 0.1.4 dated 2019-10-18
DESCRIPTION | 9 MD5 | 40 NAMESPACE | 5 NEWS.md | 24 R/class_brain.R | 18 R/class_multibrain.R | 4 R/fs_brain.R | 504 + R/geom_abstract.R | 9 R/geom_datacube2.R |only R/loaders.R | 4 R/threejs_brain.R | 47 R/utils.R | 5 R/utils_orient.R |only R/zzz.R |only inst/WORDLIST | 61 inst/htmlwidgets/lib/dipterixThreeBrain-1.0.1/dipterix.css | 16 inst/htmlwidgets/lib/dipterixThreeBrain-1.0.1/main.js | 3618 +++++++------ inst/htmlwidgets/threejs_brain.js | 54 man/DataCubeGeom2.Rd |only man/check_freesurfer_path.Rd |only man/freesurfer_brain.Rd | 15 man/read_gii2.Rd |only man/read_mgz.Rd |only man/reorient_volume.Rd |only man/threejs_brain.Rd | 19 25 files changed, 2720 insertions(+), 1732 deletions(-)
Title: 'GeoNetwork' API R Interface
Description: Provides an R interface to the 'GeoNetwork' API (<https://geonetwork-opensource.org/#api>) allowing to upload and publish metadata in a 'GeoNetwork' web-application and exposte it to OGC CSW.
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>)
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between geonapi versions 0.2-1 dated 2019-05-26 and 0.2-2 dated 2019-10-18
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/GNManager.R | 23 ++++++++++++++--------- R/geonapi.R | 4 ++-- README.md | 2 +- man/GNManager.Rd | 12 ++++++++---- man/geonapi.Rd | 4 ++-- 7 files changed, 37 insertions(+), 28 deletions(-)
Title: Causal Effect Identification from Multiple Incomplete Data
Sources
Description: Identification of causal effects from arbitrary observational and experimental probability
distributions via do-calculus and standard probability manipulations using a search-based algorithm.
Allows for the presence of mechanisms related to selection bias (Bareinboim, E. and Tian, J. (2015)
<http://ftp.cs.ucla.edu/pub/stat_ser/r445.pdf>), transportability (Bareinboim, E. and Pearl, J. (2014)
<http://ftp.cs.ucla.edu/pub/stat_ser/r443.pdf>), missing data (Mohan, K. and Pearl, J. and Tian., J.
(2013) <http://ftp.cs.ucla.edu/pub/stat_ser/r410.pdf>) and arbitrary combinations of these. Also supports
identification in the presence of context-specific independence (CSI) relations through labeled directed
acyclic graphs (LDAG). For details on CSIs see Corander et al. (2019) <doi:10.1016/j.apal.2019.04.004>.
For further information on the search-based approach see Tikka et al. (2019) <arXiv:1902.01073>.
Author: Santtu Tikka [aut, cre] (<https://orcid.org/0000-0003-4039-4342>),
Antti Hyttinen [ctb] (<https://orcid.org/0000-0002-6649-3229>),
Juha Karvanen [ctb] (<https://orcid.org/0000-0001-5530-769X>)
Maintainer: Santtu Tikka <santtuth@gmail.com>
Diff between dosearch versions 1.0.2 dated 2019-02-28 and 1.0.3 dated 2019-10-18
dosearch-1.0.2/dosearch/R/get_derivation.R |only dosearch-1.0.2/dosearch/build |only dosearch-1.0.2/dosearch/inst/doc |only dosearch-1.0.2/dosearch/man/get_derivation.Rd |only dosearch-1.0.2/dosearch/src/formulasearch.cpp |only dosearch-1.0.2/dosearch/src/formulasearch.h |only dosearch-1.0.2/dosearch/vignettes |only dosearch-1.0.3/dosearch/DESCRIPTION | 16 dosearch-1.0.3/dosearch/MD5 | 58 - dosearch-1.0.3/dosearch/NAMESPACE | 6 dosearch-1.0.3/dosearch/NEWS | 20 dosearch-1.0.3/dosearch/R/RcppExports.R | 18 dosearch-1.0.3/dosearch/R/dosearch.R |only dosearch-1.0.3/dosearch/R/get_derivation_dag.R |only dosearch-1.0.3/dosearch/R/get_derivation_ldag.R |only dosearch-1.0.3/dosearch/R/to_dec.R |only dosearch-1.0.3/dosearch/R/to_vec.R |only dosearch-1.0.3/dosearch/inst/CITATION |only dosearch-1.0.3/dosearch/man/bivariate_missingness.Rd | 44 dosearch-1.0.3/dosearch/man/dosearch-package.Rd | 231 ++-- dosearch-1.0.3/dosearch/man/dosearch.Rd |only dosearch-1.0.3/dosearch/src/RcppExports.cpp | 45 dosearch-1.0.3/dosearch/src/csisearch.cpp |only dosearch-1.0.3/dosearch/src/csisearch.h |only dosearch-1.0.3/dosearch/src/dcongraph.h | 4 dosearch-1.0.3/dosearch/src/derivation.h | 2 dosearch-1.0.3/dosearch/src/dosearch.cpp | 1070 +++++++++++++++++-- dosearch-1.0.3/dosearch/src/dosearch.h |only dosearch-1.0.3/dosearch/src/initialize_csisearch.cpp |only dosearch-1.0.3/dosearch/src/initialize_dosearch.cpp |only dosearch-1.0.3/dosearch/src/ldag.cpp |only dosearch-1.0.3/dosearch/src/ldag.h |only dosearch-1.0.3/dosearch/src/search.cpp |only dosearch-1.0.3/dosearch/src/search.h |only dosearch-1.0.3/dosearch/src/set.cpp | 8 dosearch-1.0.3/dosearch/src/set.h | 3 36 files changed, 1247 insertions(+), 278 deletions(-)
Title: Clusters of Colocalized Sequences
Description: Also abbreviates to "CCSeq". Finds clusters of colocalized sequences in .bed annotation files
up to a specified cut-off distance. Two sequences are colocalized if they
are within the cut-off distance of each other, and clusters are sets of
sequences where each sequence is colocalized to at least one other sequence
in the cluster. For a set of .bed annotation tables provided in a list
along with a cut-off distance, the program will output a file containing
the locations of each cluster. Annotated .bed files are from
the 'pwmscan' application at <https://ccg.epfl.ch/pwmtools/pwmscan.php>.
Personal machines might crash or take excessively long depending
on the number of annotated sequences in each file and whether chromsearch()
or gensearch() is used.
Author: Stefan Golas [cre, aut]
Maintainer: Stefan Golas <stefanmgolas@gmail.com>
Diff between colocalized versions 0.1.0 dated 2019-09-19 and 0.2.0 dated 2019-10-18
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/chromsearch.R | 11 ++++++++--- R/gensearch.R | 16 ++++++++++++---- 4 files changed, 28 insertions(+), 15 deletions(-)
Title: Analysis of Diversity
Description: Functions, data sets and examples for the calculation of various indices of biodiversity including species, functional and phylogenetic diversity. Part of the indices are expressed in terms of equivalent numbers of species. The package also provides ways to partition biodiversity across spatial or temporal scales (alpha, beta, gamma diversities). In addition to the quantification of biodiversity, ordination approaches are available which rely on diversity indices and allow the detailed identification of species, functional or phylogenetic differences between communities.
Author: Sandrine Pavoine
Maintainer: Sandrine Pavoine <sandrine.pavoine@mnhn.fr>
Diff between adiv versions 1.2 dated 2018-08-24 and 1.3 dated 2019-10-18
DESCRIPTION | 16 ++-- MD5 | 150 ++++++++++++++++++++++++------------------- NAMESPACE | 9 ++ R/PADDis.R | 7 +- R/abgdivparam.R |only R/abgevodivparam.R | 4 - R/dissABC.R | 4 - R/distinctDis.R | 24 +++++- R/distinctTopo.R | 11 +-- R/distinctUltra.R | 10 +- R/divparam.R | 16 +++- R/dspca.R |only R/eveparam.R | 16 +++- R/evodiss.R | 12 +-- R/evodiss_family.R | 71 ++++++++++++-------- R/evodiv.R |only R/evodivparam.R | 7 +- R/evoeveparam.R |only R/evouniparam.R |only R/generalized_Tradidiss.R |only R/plot.abgdivparam.R |only R/plot.decdiv.R | 80 ++++++++++++---------- R/plot.divparam.R | 6 - R/plot.dspca.R |only R/plot.eveparam.R | 6 - R/plot.evodivparam.R | 6 - R/plot.evoeveparam.R |only R/plot.evouniparam.R |only R/plot.rlqESLTP.R | 47 ++++++++----- R/qDT.R |only R/qHdiv.R | 4 - R/speciesdiv.R | 2 R/treeUniqueness.R |only R/uniqueness.R | 12 ++- build/partial.rdb |binary man/CF.Rd | 8 +- man/EH.Rd | 16 ++-- man/EqRao.Rd | 32 +++++---- man/K.Rd | 47 ++++++++++--- man/PADDis.Rd | 18 ++--- man/QE.Rd | 33 +++++++-- man/RP15JVS.Rd | 2 man/RPP16EE.Rd | 12 +++ man/Rentropy.Rd | 16 ++++ man/abgdivparam.Rd |only man/abgevodivparam.Rd | 44 +++++++----- man/adiv-package.Rd | 2 man/aptree.Rd | 25 ++++--- man/batcomm.Rd | 8 +- man/betastat.Rd | 14 ++-- man/birdData.Rd | 8 +- man/crossdpcoa.Rd | 46 +++++++++---- man/decdiv.Rd | 31 ++++---- man/dissABC.Rd | 17 ++-- man/dissRicotta.Rd | 12 ++- man/distinctDis.Rd | 12 ++- man/distinctTopo.Rd | 16 ++-- man/distinctTree.Rd | 15 ++-- man/distinctUltra.Rd | 16 ++-- man/divparam.Rd | 25 ++++--- man/dsimcom.Rd | 13 ++- man/dspca.Rd |only man/eveparam.Rd | 25 ++++--- man/evoCA.Rd | 47 ++++++++----- man/evoNSCA.Rd | 47 ++++++++----- man/evodiss.Rd | 16 +++- man/evodiss_family.Rd | 54 +++++++++------ man/evodiv.Rd |only man/evodivparam.Rd | 38 +++++++--- man/evoeveparam.Rd |only man/evopca.Rd | 53 ++++++++------- man/evouniparam.Rd |only man/generalized_Tradidiss.Rd |only man/optimEH.Rd | 15 ++-- man/orisaved.Rd | 13 ++- man/qDT.Rd |only man/qHdiv.Rd | 35 +++++----- man/randEH.Rd | 15 ++-- man/rare_Rao.Rd | 22 +++++- man/rlqESLTP.Rd | 20 ++++- man/rockfish.Rd | 10 ++ man/speciesdiv.Rd | 12 ++- man/specieseve.Rd | 18 ++--- man/treeUniqueness.Rd |only man/twoHmax.Rd | 24 ++++-- man/uniqueness.Rd | 21 +++--- 86 files changed, 929 insertions(+), 564 deletions(-)
Title: DBI Connector to Presto
Description: Implements a 'DBI' compliant interface to Presto. Presto is
an open source distributed SQL query engine for running interactive
analytic queries against data sources of all sizes ranging from
gigabytes to petabytes: <https://prestodb.io/>.
Author: Onur Ismail Filiz [aut, cre],
Sergey Goder [aut],
John Myles White [ctb]
Maintainer: Onur Ismail Filiz <onur@fb.com>
Diff between RPresto versions 1.3.3 dated 2019-05-03 and 1.3.4 dated 2019-10-18
DESCRIPTION | 6 MD5 | 164 +++++++------- NEWS.md | 5 R/Presto.R | 5 R/PrestoConnection.R | 5 R/PrestoCursor.R | 5 R/PrestoDriver.R | 5 R/PrestoResult.R | 5 R/PrestoSession.R | 5 R/copy.to.src.presto.R | 5 R/db.data.type.PrestoConnection.R | 5 R/db.explain.PrestoConnection.R | 5 R/db.query.rows.PrestoConnection.R | 5 R/dbClearResult.R | 5 R/dbConnect.R | 5 R/dbDataType.R | 5 R/dbDisconnect.R | 5 R/dbExistsTable.R | 5 R/dbFetch.R | 5 R/dbGetInfo.R | 5 R/dbGetQuery.R | 5 R/dbGetRowCount.R | 5 R/dbGetStatement.R | 5 R/dbHasCompleted.R | 5 R/dbIsValid.R | 5 R/dbListFields.R | 5 R/dbListTables.R | 5 R/dbSendQuery.R | 5 R/dbUnloadDriver.R | 5 R/db_desc.PrestoConnection.R | 5 R/db_query_fields.R | 5 R/dbplyr_compatible.R | 5 R/description_from_info.R | 5 R/extract.data.R | 5 R/fetch.R | 5 R/help.R | 5 R/json.tabular.to.data.frame.R | 5 R/parse.response.R | 5 R/request_headers.R | 5 R/sql_translate_env.R | 13 - R/src.presto.R | 5 R/tbl.src.presto.R | 5 R/utility_functions.R | 5 README.md | 2 src/check_names.cpp | 3 src/transpose.cpp | 3 tests/testthat.R | 5 tests/testthat/test-PrestoCursor.R | 5 tests/testthat/test-bigint_handling.R | 5 tests/testthat/test-check.status.code.R | 8 tests/testthat/test-data_types.R | 5 tests/testthat/test-dbClearResult.R | 5 tests/testthat/test-dbConnect.R | 5 tests/testthat/test-dbDataType.R | 5 tests/testthat/test-dbDisconnect.R | 5 tests/testthat/test-dbExistsTable.R | 5 tests/testthat/test-dbFetch.R | 5 tests/testthat/test-dbGetInfo.R | 5 tests/testthat/test-dbGetQuery.R | 5 tests/testthat/test-dbGetRowCount.R | 5 tests/testthat/test-dbGetStatement.R | 5 tests/testthat/test-dbHasCompleted.R | 5 tests/testthat/test-dbIsValid.R | 5 tests/testthat/test-dbListFields.R | 5 tests/testthat/test-dbListTables.R | 5 tests/testthat/test-dbSendQuery.R | 5 tests/testthat/test-dbUnloadDriver.R | 5 tests/testthat/test-db_explain.R | 5 tests/testthat/test-db_query_fields.R | 5 tests/testthat/test-dplyr.integration.R | 5 tests/testthat/test-dplyr_as_type.R | 5 tests/testthat/test-extract.data.R | 5 tests/testthat/test-fetch.R | 5 tests/testthat/test-get.state.R | 5 tests/testthat/test-integration.R | 9 tests/testthat/test-json_tabular_to_data_frame.R | 5 tests/testthat/test-response.to.content.R | 5 tests/testthat/test-session.property.R | 5 tests/testthat/test-session.timezone.R | 5 tests/testthat/test-stop.with.error.message.R | 5 tests/testthat/test-tbl.src_presto.R | 23 +- tests/testthat/test-translate_sql.R | 253 ++++++++++++++++++++--- tests/testthat/utilities.R | 5 83 files changed, 502 insertions(+), 347 deletions(-)
Title: Doubly Truncated Data Analysis, Cumulative Incidence Functions
Description: Nonparametric estimator of the cumulative incidences of competing risks under double truncation. The estimator generalizes the Efron-Petrosian NPMLE (Non-Parametric Maximun Likelihood Estimator) to the competing risks setting. Efron, B. and Petrosian, V. (1999) <doi:10.2307/2669997>.
Author: Jacobo de Uña Álvarez [aut],
José Carlos Soage González [cre]
Maintainer: José Carlos Soage González <jsoage@uvigo.es>
Diff between DTDA.cif versions 1.0 dated 2019-08-02 and 1.0.1 dated 2019-10-18
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/DTDAcif-package.R | 2 +- R/DTDAcif.R | 4 ++-- man/DTDA.cif-package.Rd | 2 +- 5 files changed, 11 insertions(+), 11 deletions(-)
Title: Performs a BLP Demand Estimation
Description: Provides the estimation algorithm to perform the demand estimation described in Berry, Levinsohn and Pakes (1995) <DOI:10.2307/2171802> . The routine uses analytic gradients and offers a large number of implemented integration methods and optimization routines.
Author: Daniel Brunner (aut), Constantin Weiser (ctr), Andre Romahn (ctr)
Maintainer: Daniel Brunner <daniel.brunner@hhu.de>
Diff between BLPestimatoR versions 0.2.9 dated 2019-05-14 and 0.3.0 dated 2019-10-18
BLPestimatoR-0.2.9/BLPestimatoR/R/nevo.R |only BLPestimatoR-0.2.9/BLPestimatoR/data/demographicData.rda |only BLPestimatoR-0.2.9/BLPestimatoR/data/originalDraws.rda |only BLPestimatoR-0.2.9/BLPestimatoR/data/productData.rda |only BLPestimatoR-0.2.9/BLPestimatoR/data/theta_guesses.rda |only BLPestimatoR-0.2.9/BLPestimatoR/data/w_guesses.rda |only BLPestimatoR-0.2.9/BLPestimatoR/man/demographicData.Rd |only BLPestimatoR-0.2.9/BLPestimatoR/man/originalDraws.Rd |only BLPestimatoR-0.2.9/BLPestimatoR/man/productData.Rd |only BLPestimatoR-0.2.9/BLPestimatoR/man/theta_guesses.Rd |only BLPestimatoR-0.2.9/BLPestimatoR/man/w_guesses.Rd |only BLPestimatoR-0.3.0/BLPestimatoR/DESCRIPTION | 9 BLPestimatoR-0.3.0/BLPestimatoR/MD5 | 45 BLPestimatoR-0.3.0/BLPestimatoR/NAMESPACE | 1 BLPestimatoR-0.3.0/BLPestimatoR/R/BLP_data.R | 26 BLPestimatoR-0.3.0/BLPestimatoR/R/car.R |only BLPestimatoR-0.3.0/BLPestimatoR/R/cereal.R |only BLPestimatoR-0.3.0/BLPestimatoR/R/estimateBLP.R | 10 BLPestimatoR-0.3.0/BLPestimatoR/build/vignette.rds |binary BLPestimatoR-0.3.0/BLPestimatoR/data/demographicData_cereal.rda |only BLPestimatoR-0.3.0/BLPestimatoR/data/dummies_cars.rda |only BLPestimatoR-0.3.0/BLPestimatoR/data/originalDraws_cereal.rda |only BLPestimatoR-0.3.0/BLPestimatoR/data/productData_cars.rda |only BLPestimatoR-0.3.0/BLPestimatoR/data/productData_cereal.rda |only BLPestimatoR-0.3.0/BLPestimatoR/data/theta_guesses_cereal.rda |only BLPestimatoR-0.3.0/BLPestimatoR/data/w_guesses_cereal.rda |only BLPestimatoR-0.3.0/BLPestimatoR/inst/doc/blp_intro.R | 405 ++ BLPestimatoR-0.3.0/BLPestimatoR/inst/doc/blp_intro.Rmd | 507 ++- BLPestimatoR-0.3.0/BLPestimatoR/inst/doc/blp_intro.html | 1444 ++++++---- BLPestimatoR-0.3.0/BLPestimatoR/man/demographicData_cereal.Rd |only BLPestimatoR-0.3.0/BLPestimatoR/man/dummies_cars.Rd |only BLPestimatoR-0.3.0/BLPestimatoR/man/originalDraws_cereal.Rd |only BLPestimatoR-0.3.0/BLPestimatoR/man/productData_cars.Rd |only BLPestimatoR-0.3.0/BLPestimatoR/man/productData_cereal.Rd |only BLPestimatoR-0.3.0/BLPestimatoR/man/theta_guesses_cereal.Rd |only BLPestimatoR-0.3.0/BLPestimatoR/man/w_guesses_cereal.Rd |only BLPestimatoR-0.3.0/BLPestimatoR/vignettes/blp_intro.Rmd | 507 ++- 37 files changed, 2086 insertions(+), 868 deletions(-)
Title: Memory-Efficient, Visualize-Enhanced, Parallel-Accelerated GWAS
Tool
Description: A memory-efficient, visualize-enhanced, parallel-accelerated Genome-Wide Association Study (GWAS) tool. It can
(1) effectively process large data,
(2) rapidly evaluate population structure,
(3) efficiently estimate variance components several algorithms,
(4) implement parallel-accelerated association tests of markers three methods,
(5) globally efficient design on GWAS process computing,
(6) enhance visualization of related information.
'rMVP' contains three models GLM (Alkes Price (2006) <DOI:10.1038/ng1847>), MLM (Jianming Yu (2006) <DOI:10.1038/ng1702>)
and FarmCPU (Xiaolei Liu (2016) <doi:10.1371/journal.pgen.1005767>); variance components estimation methods EMMAX
(Hyunmin Kang (2008) <DOI:10.1534/genetics.107.080101>;), FaSTLMM (method: Christoph Lippert (2011) <DOI:10.1038/nmeth.1681>,
R implementation from 'GAPIT2': You Tang and Xiaolei Liu (2016) <DOI:10.1371/journal.pone.0107684> and
'SUPER': Qishan Wang and Feng Tian (2014) <DOI:10.1371/journal.pone.0107684>), and HE regression
(Xiang Zhou (2017) <DOI:10.1214/17-AOAS1052>).
Author: Lilin Yin [aut],
Haohao Zhang [aut],
Zhenshuang Tang [aut],
Jingya Xu [aut],
Dong Yin [aut],
Zhiwu Zhang [aut],
Xiaohui Yuan [aut],
Mengjin Zhu [aut],
Shuhong Zhao [aut],
Xinyun Li [aut],
Qishan Wang [ctb],
Feng Tian [ctb],
Hyunmin Kang [ctb],
Xiang Zhou [ctb],
Xiaolei Liu [cre, aut, cph]
Maintainer: Xiaolei Liu <xiaoleiliu@mail.hzau.edu.cn>
Diff between rMVP versions 0.99.16 dated 2019-09-24 and 0.99.17 dated 2019-10-18
DESCRIPTION | 8 +-- MD5 | 10 ++-- R/MVP.Utility.r | 4 - R/MVP.r | 34 ++++++++++++--- inst/extdata/03_hapmap/mvp.hmp.txt | 80 ++++++++++++++++++------------------- src/data_converter.cpp | 29 ++++++++----- 6 files changed, 98 insertions(+), 67 deletions(-)
Title: Functional Programming Tools
Description: A complete and consistent functional programming toolkit for R.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
RStudio [cph, fnd]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between purrr versions 0.3.2 dated 2019-03-15 and 0.3.3 dated 2019-10-18
DESCRIPTION | 8 - MD5 | 75 +++++++++--------- NEWS.md | 12 ++ R/as_mapper.R | 2 R/compat-lifecycle.R | 6 + R/detect.R | 6 - R/flatten.R | 4 R/map.R | 154 +++++++++++++++++++++---------------- R/modify.R | 4 R/partial.R | 4 R/prepend.R | 10 +- R/utils.R | 6 - README.md | 6 - build/purrr.pdf |binary build/vignette.rds |binary inst/doc/other-langs.html | 9 +- man/as_mapper.Rd | 2 man/at_depth.Rd | 4 man/detect.Rd | 6 - man/flatten.Rd | 4 man/imap.Rd | 3 man/invoke.Rd | 4 man/lmap.Rd | 3 man/map.Rd | 117 +++++++--------------------- man/map2.Rd | 3 man/map_if.Rd |only man/modify.Rd | 3 man/partial.Rd | 2 man/prepend.Rd | 6 - tests/testthat/helper-conditions.R | 13 +++ tests/testthat/test-chuck.R | 2 tests/testthat/test-flatten.R | 10 +- tests/testthat/test-map.R | 6 - tests/testthat/test-map2.R | 6 - tests/testthat/test-map_n.R | 6 - tests/testthat/test-partial.R | 2 tests/testthat/test-pluck.R | 12 +- tests/testthat/test-prepend.R | 24 +++++ tests/testthat/test-transpose.R | 8 - 39 files changed, 299 insertions(+), 253 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-03-13 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-08-29 0.2.4
2018-10-13 0.2.3
2018-07-24 0.2.2
2018-05-26 0.2.1
2018-04-22 0.2.0
2018-01-07 0.1.5
2017-11-23 0.1.4
2017-11-21 0.1.3
2017-09-09 0.1.2
2017-08-16 0.1.1
Title: Weaning Age Reconstruction with Nitrogen Isotope Analysis
Description: This estimates precise weaning ages
for a given skeletal population
by analyzing the stable nitrogen isotope ratios of them.
Bone collagen turnover rates estimated anew and
the approximate Bayesian computation (ABC)
were adopted in this package.
Author: Takumi Tsutaya
Maintainer: Takumi Tsutaya <tsutayatakumi@gmail.com>
Diff between WARN versions 1.2-3 dated 2017-12-08 and 1.2-4 dated 2019-10-18
ChangeLog | 4 DESCRIPTION | 8 - MD5 | 32 ++--- NEWS | 4 R/warn.R | 265 +++++++++++++++++++++++++++--------------------- R/warn_s3.R | 24 +++- man/WARN-package.Rd | 7 - man/lerna.Rd | 1 man/plot.warn.Rd | 1 man/plot.warnCI.Rd | 1 man/plot.warnProb.Rd | 1 man/summary.warn.Rd | 1 man/summary.warnProb.Rd | 1 man/warn.Rd | 14 +- man/warnCI.Rd | 3 man/warnOptim.Rd | 13 +- man/warnProb.Rd | 3 17 files changed, 228 insertions(+), 155 deletions(-)
Title: Hypothesis Matrix Translation
Description: Translation between experimental null hypotheses, hypothesis matrices, and contrast matrices as used in linear regression models. The package is based on the method described in Schad, Vasishth, Hohenstein, and Kliegl (2019) <doi:10.1016/j.jml.2019.104038>.
Author: Maximilian M. Rabe [aut, cre],
Shravan Vasishth [aut],
Sven Hohenstein [aut],
Reinhold Kliegl [aut],
Daniel J. Schad [aut]
Maintainer: Maximilian M. Rabe <maximilian.rabe@uni-potsdam.de>
Diff between hypr versions 0.1.2 dated 2019-10-09 and 0.1.3 dated 2019-10-18
hypr-0.1.2/hypr/R/hello.R |only hypr-0.1.3/hypr/DESCRIPTION | 14 - hypr-0.1.3/hypr/MD5 | 34 ++- hypr-0.1.3/hypr/NAMESPACE | 5 hypr-0.1.3/hypr/R/equations.R | 4 hypr-0.1.3/hypr/R/hypr.R | 364 ++++++++++++++++++++++++++----------- hypr-0.1.3/hypr/README.md | 2 hypr-0.1.3/hypr/build |only hypr-0.1.3/hypr/inst/CITATION | 2 hypr-0.1.3/hypr/inst/doc |only hypr-0.1.3/hypr/man/cmat.Rd | 27 ++ hypr-0.1.3/hypr/man/conversions.Rd | 7 hypr-0.1.3/hypr/man/hypr-class.Rd | 30 ++- hypr-0.1.3/hypr/man/hypr.Rd | 45 +++- hypr-0.1.3/hypr/vignettes |only 15 files changed, 385 insertions(+), 149 deletions(-)
Title: Time Series Regression Models with Distributed Lag Models
Description: Provides time series regression models with one predictor using finite distributed lag models, polynomial (Almon) distributed lag models, geometric distributed lag models with Koyck transformation, and autoregressive distributed lag models. It also consists of functions for computation of h-step ahead forecasts from these models. See Baltagi (2011) <doi:10.1007/978-3-642-20059-5> for more information.
Author: Haydar Demirhan [aut, cre, cph] (<https://orcid.org/0000-0002-8565-4710>)
Maintainer: Haydar Demirhan <haydar.demirhan@rmit.edu.au>
Diff between dLagM versions 1.0.17 dated 2019-08-24 and 1.0.18 dated 2019-10-18
dLagM-1.0.17/dLagM/R/MASE.R |only dLagM-1.0.17/dLagM/R/sortScore.default.R |only dLagM-1.0.17/dLagM/R/sortScore.main.R |only dLagM-1.0.18/dLagM/DESCRIPTION | 8 - dLagM-1.0.18/dLagM/MD5 | 46 ++--- dLagM-1.0.18/dLagM/NAMESPACE | 7 dLagM-1.0.18/dLagM/NEWS.md | 6 dLagM-1.0.18/dLagM/R/GoFs.R |only dLagM-1.0.18/dLagM/R/ardlBound.R | 29 ++- dLagM-1.0.18/dLagM/R/ardlBoundOrders.R | 213 +++++++++++++++++---------- dLagM-1.0.18/dLagM/R/ardlDlmForecast.main.R | 9 - dLagM-1.0.18/dLagM/R/dlm.main.R | 6 dLagM-1.0.18/dLagM/R/finiteDLMauto.R | 2 dLagM-1.0.18/dLagM/R/finiteDLMauto.default.R | 2 dLagM-1.0.18/dLagM/R/finiteDLMauto.main.R | 24 ++- dLagM-1.0.18/dLagM/R/forecast.ardlDlm.R | 4 dLagM-1.0.18/dLagM/R/rolCorplot.R | 4 dLagM-1.0.18/dLagM/R/sortScore.R | 23 ++ dLagM-1.0.18/dLagM/build/partial.rdb |binary dLagM-1.0.18/dLagM/man/MASE.Rd | 37 +++- dLagM-1.0.18/dLagM/man/ardlBound.Rd | 12 + dLagM-1.0.18/dLagM/man/ardlBoundOrders.Rd | 13 + dLagM-1.0.18/dLagM/man/dLagM-package.Rd | 8 - dLagM-1.0.18/dLagM/man/finiteDLMauto.Rd | 9 - dLagM-1.0.18/dLagM/man/rolCorPlot.Rd | 5 dLagM-1.0.18/dLagM/man/sort.score.Rd | 10 - 26 files changed, 317 insertions(+), 160 deletions(-)
Title: Methods for Dimension Reduction
Description: Functions for dimension reduction, using MAVE (Minimum Average Variance Estimation), OPG (Outer Product of Gradient) and KSIR (sliced inverse regression of kernel version). Methods for selecting the best dimension are also included. Xia (2002) <doi:10.1111/1467-9868.03411>; Xia (2007) <doi:10.1214/009053607000000352>; Wang (2008) <doi:10.1198/016214508000000418>.
Author: Hang Weiqiang<E0010758@u.nus.edu>, Xia Yingcun<staxyc@nus.edu.sg>
Maintainer: Hang Weiqiang<E0010758@u.nus.edu>
Diff between MAVE versions 1.3.9 dated 2019-05-08 and 1.3.10 dated 2019-10-18
DESCRIPTION | 8 MD5 | 14 - R/MAVE.R | 329 ++++++++++++++++---------------- R/MAVE_CV.R | 106 +++++----- R/coef_mave.R | 3 R/print_mave_cv.R | 57 ++--- inst/doc/User_Guild_of_Package_MAVE.pdf |binary man/mave.dim.Rd | 5 8 files changed, 271 insertions(+), 251 deletions(-)
Title: R Code for Stock Synthesis
Description: A collection of R functions for use with Stock Synthesis, a
fisheries stock assessment modeling platform written in ADMB by Dr. Richard
D. Methot at the NOAA Northwest Fisheries Science Center. The functions
include tools for summarizing and plotting results, manipulating files,
visualizing model parameterizations, and various other common stock
assessment tasks.
Author: Ian G. Taylor, Ian J. Stewart, Allan C. Hicks, Tommy M. Garrison,
Andre E. Punt, John R. Wallace, Chantel R. Wetzel, James T. Thorson,
Yukio Takeuchi, Kotaro Ono, Cole C. Monnahan, Christine C. Stawitz,
Z. Teresa A'mar, Athol R. Whitten, Kelli F. Johnson, Robbie L. Emmet,
Sean C. Anderson, Gwladys I. Lambert, Megan M. Stachura,
Andrew B. Cooper, Andi Stephens, Neil L. Klaer, Carey R. McGilliard,
Iago Mosqueira, Watal M. Iwasaki, Kathryn Doering, and Andrea M. Havron
Maintainer: Ian G. Taylor <Ian.Taylor@noaa.gov>
Diff between r4ss versions 1.24.0 dated 2015-12-23 and 1.36.1 dated 2019-10-18
r4ss-1.24.0/r4ss/R/IOTCmove.R |only r4ss-1.24.0/r4ss/R/SSFishGraph.R |only r4ss-1.24.0/r4ss/R/SS_write_length.fit.R |only r4ss-1.24.0/r4ss/R/SSchangeYears.R |only r4ss-1.24.0/r4ss/R/SSplotCohorts.R |only r4ss-1.24.0/r4ss/R/addSSsummarize.R |only r4ss-1.24.0/r4ss/R/movepars.R |only r4ss-1.24.0/r4ss/R/sel.line.R |only r4ss-1.24.0/r4ss/R/selfit.R |only r4ss-1.24.0/r4ss/R/selfit_spline.R |only r4ss-1.24.0/r4ss/R/update_r4ss_files.R |only r4ss-1.24.0/r4ss/man/IOTCmove.Rd |only r4ss-1.24.0/r4ss/man/SSFishGraph.Rd |only r4ss-1.24.0/r4ss/man/SS_write_length.fit.Rd |only r4ss-1.24.0/r4ss/man/SSplotCohorts.Rd |only r4ss-1.24.0/r4ss/man/addSSsummarize.Rd |only r4ss-1.24.0/r4ss/man/movepars.Rd |only r4ss-1.24.0/r4ss/man/sel.line.Rd |only r4ss-1.24.0/r4ss/man/selfit.Rd |only r4ss-1.24.0/r4ss/man/selfit_spline.Rd |only r4ss-1.24.0/r4ss/man/update_r4ss_files.Rd |only r4ss-1.36.1/r4ss/DESCRIPTION | 24 r4ss-1.36.1/r4ss/MD5 | 361 +-- r4ss-1.36.1/r4ss/NAMESPACE | 46 r4ss-1.36.1/r4ss/NEWS.md | 43 r4ss-1.36.1/r4ss/R/NegLogInt_Fn.R | 239 +- r4ss-1.36.1/r4ss/R/PinerPlot.R | 72 r4ss-1.36.1/r4ss/R/RebuildPlot.R | 3 r4ss-1.36.1/r4ss/R/SSMethod.Cond.TA1.8.R | 141 - r4ss-1.36.1/r4ss/R/SSMethod.TA1.8.R | 213 + r4ss-1.36.1/r4ss/R/SS_ForeCatch.R | 68 r4ss-1.36.1/r4ss/R/SS_RunJitter.R | 166 - r4ss-1.36.1/r4ss/R/SS_changepars.R | 195 + r4ss-1.36.1/r4ss/R/SS_decision_table_stuff.R | 4 r4ss-1.36.1/r4ss/R/SS_doRetro.R | 94 r4ss-1.36.1/r4ss/R/SS_fitbiasramp.R | 201 + r4ss-1.36.1/r4ss/R/SS_html.R | 68 r4ss-1.36.1/r4ss/R/SS_makeHTMLdiagnostictable.R |only r4ss-1.36.1/r4ss/R/SS_output.R | 2238 +++++++++++++++----- r4ss-1.36.1/r4ss/R/SS_parlines.R | 101 r4ss-1.36.1/r4ss/R/SS_plots.R | 502 +++- r4ss-1.36.1/r4ss/R/SS_profile.R | 127 - r4ss-1.36.1/r4ss/R/SS_read_summary.R |only r4ss-1.36.1/r4ss/R/SS_readctl.R | 231 +- r4ss-1.36.1/r4ss/R/SS_readctl_3.24.R |only r4ss-1.36.1/r4ss/R/SS_readctl_3.30.R |only r4ss-1.36.1/r4ss/R/SS_readdat.R | 693 ++---- r4ss-1.36.1/r4ss/R/SS_readdat_2.00.R |only r4ss-1.36.1/r4ss/R/SS_readdat_3.00.R |only r4ss-1.36.1/r4ss/R/SS_readdat_3.24.R |only r4ss-1.36.1/r4ss/R/SS_readdat_3.30.R |only r4ss-1.36.1/r4ss/R/SS_readforecast.R | 310 ++ r4ss-1.36.1/r4ss/R/SS_readstarter.R | 62 r4ss-1.36.1/r4ss/R/SS_readwtatage.R |only r4ss-1.36.1/r4ss/R/SS_recdevs.R | 3 r4ss-1.36.1/r4ss/R/SS_splitdat.R | 6 r4ss-1.36.1/r4ss/R/SS_tune_comps.R |only r4ss-1.36.1/r4ss/R/SS_varadjust.R | 160 + r4ss-1.36.1/r4ss/R/SS_writectl.R | 120 - r4ss-1.36.1/r4ss/R/SS_writectl_3.24.R |only r4ss-1.36.1/r4ss/R/SS_writectl_3.30.R |only r4ss-1.36.1/r4ss/R/SS_writedat.R | 186 - r4ss-1.36.1/r4ss/R/SS_writedat_3.24.R |only r4ss-1.36.1/r4ss/R/SS_writedat_3.30.R |only r4ss-1.36.1/r4ss/R/SS_writeforecast.R | 145 - r4ss-1.36.1/r4ss/R/SS_writestarter.R | 13 r4ss-1.36.1/r4ss/R/SS_writewtatage.R |only r4ss-1.36.1/r4ss/R/SSbiologytables.R |only r4ss-1.36.1/r4ss/R/SSbootstrap.R | 3 r4ss-1.36.1/r4ss/R/SSexecutivesummary.r |only r4ss-1.36.1/r4ss/R/SSgetMCMC.R | 148 - r4ss-1.36.1/r4ss/R/SSgetoutput.R | 29 r4ss-1.36.1/r4ss/R/SSmohnsrho.R |only r4ss-1.36.1/r4ss/R/SSplotAgeMatrix.R |only r4ss-1.36.1/r4ss/R/SSplotBiology.R | 986 +++++--- r4ss-1.36.1/r4ss/R/SSplotCatch.R | 294 +- r4ss-1.36.1/r4ss/R/SSplotCohortCatch.R |only r4ss-1.36.1/r4ss/R/SSplotComparisons.R | 730 ++++-- r4ss-1.36.1/r4ss/R/SSplotComps.R | 1069 ++++++--- r4ss-1.36.1/r4ss/R/SSplotData.R | 386 ++- r4ss-1.36.1/r4ss/R/SSplotDiscard.R | 79 r4ss-1.36.1/r4ss/R/SSplotIndices.R | 620 +++-- r4ss-1.36.1/r4ss/R/SSplotMCMC_ExtraSelex.R | 1 r4ss-1.36.1/r4ss/R/SSplotMnwt.R | 64 r4ss-1.36.1/r4ss/R/SSplotMovementMap.R | 10 r4ss-1.36.1/r4ss/R/SSplotMovementRates.R | 86 r4ss-1.36.1/r4ss/R/SSplotNumbers.R | 577 +++-- r4ss-1.36.1/r4ss/R/SSplotPars.R | 534 ++-- r4ss-1.36.1/r4ss/R/SSplotProfile.R | 104 r4ss-1.36.1/r4ss/R/SSplotRecdevs.R | 56 r4ss-1.36.1/r4ss/R/SSplotRecdist.R | 17 r4ss-1.36.1/r4ss/R/SSplotRetroRecruits.R | 2 r4ss-1.36.1/r4ss/R/SSplotSPR.R | 36 r4ss-1.36.1/r4ss/R/SSplotSelex.R | 286 +- r4ss-1.36.1/r4ss/R/SSplotSexRatio.R |only r4ss-1.36.1/r4ss/R/SSplotSpawnrecruit.R | 287 ++ r4ss-1.36.1/r4ss/R/SSplotSummaryF.R | 23 r4ss-1.36.1/r4ss/R/SSplotTags.R | 221 + r4ss-1.36.1/r4ss/R/SSplotTimeseries.R | 141 - r4ss-1.36.1/r4ss/R/SSplotYield.R | 212 + r4ss-1.36.1/r4ss/R/SSsummarize.R | 245 +- r4ss-1.36.1/r4ss/R/SStableComparisons.R | 105 r4ss-1.36.1/r4ss/R/SStimeseries.R |only r4ss-1.36.1/r4ss/R/SSunavailableSpawningOutput.R |only r4ss-1.36.1/r4ss/R/TSCplot.R | 13 r4ss-1.36.1/r4ss/R/bubble3.R | 16 r4ss-1.36.1/r4ss/R/getADMBHessian.R | 6 r4ss-1.36.1/r4ss/R/make_multifig.R | 103 r4ss-1.36.1/r4ss/R/make_multifig_sexratio.R |only r4ss-1.36.1/r4ss/R/mcmc.nuisance.R | 1 r4ss-1.36.1/r4ss/R/mcmc.out.R | 3 r4ss-1.36.1/r4ss/R/mountains.R | 7 r4ss-1.36.1/r4ss/R/plotCI.R | 1 r4ss-1.36.1/r4ss/R/r4ss-package.R | 31 r4ss-1.36.1/r4ss/R/rich.colors.short.R | 1 r4ss-1.36.1/r4ss/R/selShapes.R |only r4ss-1.36.1/r4ss/R/stackpoly.R | 1 r4ss-1.36.1/r4ss/README.md | 51 r4ss-1.36.1/r4ss/build |only r4ss-1.36.1/r4ss/inst |only r4ss-1.36.1/r4ss/man/DoProjectPlots.Rd | 20 r4ss-1.36.1/r4ss/man/NegLogInt_Fn.Rd | 42 r4ss-1.36.1/r4ss/man/PinerPlot.Rd | 43 r4ss-1.36.1/r4ss/man/SSMethod.Cond.TA1.8.Rd | 55 r4ss-1.36.1/r4ss/man/SSMethod.TA1.8.Rd | 39 r4ss-1.36.1/r4ss/man/SS_ForeCatch.Rd | 41 r4ss-1.36.1/r4ss/man/SS_RunJitter.Rd | 35 r4ss-1.36.1/r4ss/man/SS_changepars.Rd | 73 r4ss-1.36.1/r4ss/man/SS_doRetro.Rd | 20 r4ss-1.36.1/r4ss/man/SS_fitbiasramp.Rd | 18 r4ss-1.36.1/r4ss/man/SS_html.Rd | 15 r4ss-1.36.1/r4ss/man/SS_makeHTMLdiagnostictable.Rd |only r4ss-1.36.1/r4ss/man/SS_makedatlist.Rd | 33 r4ss-1.36.1/r4ss/man/SS_output.Rd | 89 r4ss-1.36.1/r4ss/man/SS_parlines.Rd | 23 r4ss-1.36.1/r4ss/man/SS_plots.Rd | 119 - r4ss-1.36.1/r4ss/man/SS_profile.Rd | 52 r4ss-1.36.1/r4ss/man/SS_read_summary.Rd |only r4ss-1.36.1/r4ss/man/SS_readctl.Rd | 81 r4ss-1.36.1/r4ss/man/SS_readctl_3.24.Rd |only r4ss-1.36.1/r4ss/man/SS_readctl_3.30.Rd |only r4ss-1.36.1/r4ss/man/SS_readdat.Rd | 32 r4ss-1.36.1/r4ss/man/SS_readdat_2.00.Rd |only r4ss-1.36.1/r4ss/man/SS_readdat_3.00.Rd |only r4ss-1.36.1/r4ss/man/SS_readdat_3.24.Rd |only r4ss-1.36.1/r4ss/man/SS_readdat_3.30.Rd |only r4ss-1.36.1/r4ss/man/SS_readforecast.Rd | 26 r4ss-1.36.1/r4ss/man/SS_readstarter.Rd | 13 r4ss-1.36.1/r4ss/man/SS_readwtatage.Rd |only r4ss-1.36.1/r4ss/man/SS_recdevs.Rd | 10 r4ss-1.36.1/r4ss/man/SS_splitdat.Rd | 16 r4ss-1.36.1/r4ss/man/SS_tune_comps.Rd |only r4ss-1.36.1/r4ss/man/SS_varadjust.Rd | 41 r4ss-1.36.1/r4ss/man/SS_writectl.Rd | 39 r4ss-1.36.1/r4ss/man/SS_writectl_3.24.Rd |only r4ss-1.36.1/r4ss/man/SS_writectl_3.30.Rd |only r4ss-1.36.1/r4ss/man/SS_writedat.Rd | 39 r4ss-1.36.1/r4ss/man/SS_writedat_3.24.Rd |only r4ss-1.36.1/r4ss/man/SS_writedat_3.30.Rd |only r4ss-1.36.1/r4ss/man/SS_writeforecast.Rd | 20 r4ss-1.36.1/r4ss/man/SS_writestarter.Rd | 14 r4ss-1.36.1/r4ss/man/SS_writewtatage.Rd |only r4ss-1.36.1/r4ss/man/SSbiologytables.Rd |only r4ss-1.36.1/r4ss/man/SSbootstrap.Rd | 9 r4ss-1.36.1/r4ss/man/SSexecutivesummary.Rd |only r4ss-1.36.1/r4ss/man/SSgetMCMC.Rd | 28 r4ss-1.36.1/r4ss/man/SSgetoutput.Rd | 12 r4ss-1.36.1/r4ss/man/SSmakeMmatrix.Rd | 1 r4ss-1.36.1/r4ss/man/SSmohnsrho.Rd |only r4ss-1.36.1/r4ss/man/SSplotAgeMatrix.Rd |only r4ss-1.36.1/r4ss/man/SSplotBiology.Rd | 82 r4ss-1.36.1/r4ss/man/SSplotCatch.Rd | 37 r4ss-1.36.1/r4ss/man/SSplotCohortCatch.Rd |only r4ss-1.36.1/r4ss/man/SSplotComparisons.Rd | 121 - r4ss-1.36.1/r4ss/man/SSplotComps.Rd | 53 r4ss-1.36.1/r4ss/man/SSplotData.Rd | 39 r4ss-1.36.1/r4ss/man/SSplotDiscard.Rd | 25 r4ss-1.36.1/r4ss/man/SSplotIndices.Rd | 55 r4ss-1.36.1/r4ss/man/SSplotMCMC_ExtraSelex.Rd | 3 r4ss-1.36.1/r4ss/man/SSplotMnwt.Rd | 12 r4ss-1.36.1/r4ss/man/SSplotMovementMap.Rd | 11 r4ss-1.36.1/r4ss/man/SSplotMovementRates.Rd | 24 r4ss-1.36.1/r4ss/man/SSplotNumbers.Rd | 27 r4ss-1.36.1/r4ss/man/SSplotPars.Rd | 93 r4ss-1.36.1/r4ss/man/SSplotProfile.Rd | 67 r4ss-1.36.1/r4ss/man/SSplotRecdevs.Rd | 22 r4ss-1.36.1/r4ss/man/SSplotRecdist.Rd | 12 r4ss-1.36.1/r4ss/man/SSplotRetroRecruits.Rd | 12 r4ss-1.36.1/r4ss/man/SSplotSPR.Rd | 8 r4ss-1.36.1/r4ss/man/SSplotSelex.Rd | 30 r4ss-1.36.1/r4ss/man/SSplotSexRatio.Rd |only r4ss-1.36.1/r4ss/man/SSplotSpawnrecruit.Rd | 65 r4ss-1.36.1/r4ss/man/SSplotSummaryF.Rd | 13 r4ss-1.36.1/r4ss/man/SSplotTags.Rd | 25 r4ss-1.36.1/r4ss/man/SSplotTimeseries.Rd | 21 r4ss-1.36.1/r4ss/man/SSplotYield.Rd | 35 r4ss-1.36.1/r4ss/man/SSsummarize.Rd | 15 r4ss-1.36.1/r4ss/man/SStableComparisons.Rd | 19 r4ss-1.36.1/r4ss/man/SStimeseries.Rd |only r4ss-1.36.1/r4ss/man/SSunavailableSpawningOutput.Rd |only r4ss-1.36.1/r4ss/man/TSCplot.Rd | 15 r4ss-1.36.1/r4ss/man/bubble3.Rd | 21 r4ss-1.36.1/r4ss/man/getADMBHessian.Rd | 11 r4ss-1.36.1/r4ss/man/make_multifig.Rd | 46 r4ss-1.36.1/r4ss/man/make_multifig_sexratio.Rd |only r4ss-1.36.1/r4ss/man/mcmc.nuisance.Rd | 8 r4ss-1.36.1/r4ss/man/mcmc.out.Rd | 19 r4ss-1.36.1/r4ss/man/mountains.Rd | 8 r4ss-1.36.1/r4ss/man/plotCI.Rd | 9 r4ss-1.36.1/r4ss/man/r4ss-package.Rd | 24 r4ss-1.36.1/r4ss/man/r4ss_logo.Rd | 1 r4ss-1.36.1/r4ss/man/read.admbFit.Rd | 7 r4ss-1.36.1/r4ss/man/rich.colors.short.Rd | 2 r4ss-1.36.1/r4ss/man/selShapes.Rd |only r4ss-1.36.1/r4ss/man/stackpoly.Rd | 12 r4ss-1.36.1/r4ss/vignettes |only 216 files changed, 10613 insertions(+), 6014 deletions(-)
Title: Read Large Text Files
Description: Read large text files by splitting them in smaller files.
Package 'bigreadr' also provides some convenient wrappers around fread()
and fwrite() from package 'data.table'.
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Diff between bigreadr versions 0.1.11 dated 2019-10-16 and 0.2.0 dated 2019-10-18
DESCRIPTION | 8 +++--- MD5 | 15 ++++++------ R/bind.R | 17 +++++--------- inst/testdata/wrong_string.rds |only man/bigreadr-package.Rd | 3 +- man/cbind_df.Rd | 4 ++- man/rbind_df.Rd | 4 ++- src/nlines-split.cpp | 49 +++++++++++++++++++++-------------------- tests/testthat/test-nlines.R | 4 +++ 9 files changed, 57 insertions(+), 47 deletions(-)
Title: Solving and Optimizing Large-Scale Nonlinear Systems
Description: Barzilai-Borwein spectral methods for solving nonlinear
system of equations, and for optimizing nonlinear objective
functions subject to simple constraints. A tutorial style
introduction to this package is available in a vignette on the
CRAN download page or, when the package is loaded in an R
session, with vignette("BB").
Author: Ravi Varadhan [aut, cph, trl],
Paul Gilbert [aut, cre],
Marcos Raydan [ctb] (with co-authors, wrote original algorithms in
fortran. These provided some guidance for implementing R code in
the BB package.),
JM Martinez [ctb] (with co-authors, wrote original algorithms in
fortran. These provided some guidance for implementing R code in
the BB package.),
EG Birgin [ctb] (with co-authors, wrote original algorithms in fortran.
These provided some guidance for implementing R code in the BB
package.),
W LaCruz [ctb] (with co-authors, wrote original algorithms in fortran.
These provided some guidance for implementing R code in the BB
package.)
Maintainer: Paul Gilbert <pgilbert.ttv9z@ncf.ca>
Diff between BB versions 2014.10-1 dated 2014-11-07 and 2019.10-1 dated 2019-10-18
DESCRIPTION | 12 ++++---- MD5 | 47 +++++++++++++++++--------------- NEWS | 19 +++++++++++++ R/dfsane.R | 8 +++-- R/project.R | 57 --------------------------------------- R/sane.R | 9 ++++-- R/spg.R | 6 ++-- build |only demo/multiStart.R | 2 - inst/doc/BB.R |only inst/doc/BB.Stex | 4 +- inst/doc/BB.pdf |binary inst/doc/BB_JSS.bib | 4 +- inst/doc/BBvignetteJSS.R |only inst/doc/BBvignetteJSS.Stex | 2 - inst/doc/BBvignetteJSS.pdf |binary inst/slowTests/lower-upper.R | 5 ++- inst/slowTests/spg_constraints.R | 52 +++++++++++++++++++++-------------- man/dfsane.Rd | 4 +- man/project.Rd | 2 - man/sane.Rd | 4 +- man/spg.Rd | 4 +- tests/multiStartHDP.R | 2 - vignettes/BB.Stex | 4 +- vignettes/BB_JSS.bib | 4 +- vignettes/BBvignetteJSS.Stex | 2 - 26 files changed, 118 insertions(+), 135 deletions(-)