Title: Taxonomic Information from Around the Web
Description: Interacts with a suite of web 'APIs' for taxonomic tasks,
such as verifying species names, and getting taxonomic 'hierarchies'.
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 <myrmecocystus@gmail.com>
Diff between taxize versions 0.6.6 dated 2015-10-01 and 0.7.0 dated 2015-11-30
taxize-0.6.6/taxize/man/phylomatic_format.Rd |only taxize-0.6.6/taxize/man/phylomatic_tree-deprecated.Rd |only taxize-0.6.6/taxize/man/taxize-deprecated.Rd |only taxize-0.6.6/taxize/tests/testthat/test-phylomatic_format.R |only taxize-0.6.6/taxize/tests/testthat/test-phylomatic_tree.R |only taxize-0.7.0/taxize/DESCRIPTION | 15 taxize-0.7.0/taxize/MD5 | 471 +++++----- taxize-0.7.0/taxize/NAMESPACE | 14 taxize-0.7.0/taxize/R/children.R | 4 taxize-0.7.0/taxize/R/classification.R | 6 taxize-0.7.0/taxize/R/comm2sci.R | 4 taxize-0.7.0/taxize/R/downstream.R | 30 taxize-0.7.0/taxize/R/eubon.R |only taxize-0.7.0/taxize/R/fungorum.R |only taxize-0.7.0/taxize/R/gbif_downstream.R |only taxize-0.7.0/taxize/R/get_ids.R | 5 taxize-0.7.0/taxize/R/get_nbnid.R | 1 taxize-0.7.0/taxize/R/gisd_isinvasive.R | 1 taxize-0.7.0/taxize/R/gni_search.R | 4 taxize-0.7.0/taxize/R/gnr_resolve.R | 22 taxize-0.7.0/taxize/R/ion.R |only taxize-0.7.0/taxize/R/itis.R | 10 taxize-0.7.0/taxize/R/iucn_getname.R | 23 taxize-0.7.0/taxize/R/iucn_id.R | 15 taxize-0.7.0/taxize/R/iucn_summary.R | 7 taxize-0.7.0/taxize/R/nbn_classification.R | 1 taxize-0.7.0/taxize/R/nbn_search.R | 1 taxize-0.7.0/taxize/R/nbn_synonyms.R | 1 taxize-0.7.0/taxize/R/phylomatic_format.R | 45 taxize-0.7.0/taxize/R/phylomatic_tree.R | 185 --- taxize-0.7.0/taxize/R/ping.R | 11 taxize-0.7.0/taxize/R/resolve.R | 3 taxize-0.7.0/taxize/R/sci2comm.R | 5 taxize-0.7.0/taxize/R/synonyms.R | 4 taxize-0.7.0/taxize/R/tax_agg.R | 8 taxize-0.7.0/taxize/R/tax_rank.R | 4 taxize-0.7.0/taxize/R/taxize-package.R | 41 taxize-0.7.0/taxize/R/taxize_capwords.r | 35 taxize-0.7.0/taxize/R/taxize_cite.R | 4 taxize-0.7.0/taxize/R/tp_dist.R | 1 taxize-0.7.0/taxize/R/tp_refs.R | 1 taxize-0.7.0/taxize/R/tp_search.R | 1 taxize-0.7.0/taxize/R/tp_summary.R | 1 taxize-0.7.0/taxize/R/tp_synonyms.R | 1 taxize-0.7.0/taxize/R/ubio_synonyms.R | 2 taxize-0.7.0/taxize/R/upstream.R | 3 taxize-0.7.0/taxize/R/vascan_search.r | 1 taxize-0.7.0/taxize/R/zzz.R | 25 taxize-0.7.0/taxize/README.md | 73 - taxize-0.7.0/taxize/build/vignette.rds |binary taxize-0.7.0/taxize/inst/doc/taxize_infotable.Rmd | 2 taxize-0.7.0/taxize/inst/doc/taxize_infotable.html | 2 taxize-0.7.0/taxize/inst/doc/taxize_vignette.Rmd | 14 taxize-0.7.0/taxize/inst/doc/taxize_vignette.html | 14 taxize-0.7.0/taxize/inst/ignore/wikispecies.R |only taxize-0.7.0/taxize/inst/vign/taxize_infotable.Rmd | 2 taxize-0.7.0/taxize/inst/vign/taxize_infotable.md | 2 taxize-0.7.0/taxize/inst/vign/taxize_vignette.md | 14 taxize-0.7.0/taxize/man/apg.Rd | 2 taxize-0.7.0/taxize/man/apg_families.Rd | 2 taxize-0.7.0/taxize/man/apg_lookup.Rd | 2 taxize-0.7.0/taxize/man/apg_orders.Rd | 2 taxize-0.7.0/taxize/man/bold_search.Rd | 2 taxize-0.7.0/taxize/man/children.Rd | 7 taxize-0.7.0/taxize/man/class2tree.Rd | 2 taxize-0.7.0/taxize/man/classification.Rd | 8 taxize-0.7.0/taxize/man/col_children.Rd | 2 taxize-0.7.0/taxize/man/col_classification-defunct.Rd | 2 taxize-0.7.0/taxize/man/col_downstream.Rd | 2 taxize-0.7.0/taxize/man/col_search.Rd | 2 taxize-0.7.0/taxize/man/comm2sci.Rd | 6 taxize-0.7.0/taxize/man/downstream.Rd | 15 taxize-0.7.0/taxize/man/eol_dataobjects.Rd | 2 taxize-0.7.0/taxize/man/eol_hierarchy-defunct.Rd | 2 taxize-0.7.0/taxize/man/eol_invasive-defunct.Rd | 4 taxize-0.7.0/taxize/man/eol_pages.Rd | 2 taxize-0.7.0/taxize/man/eol_search.Rd | 2 taxize-0.7.0/taxize/man/eubon.Rd |only taxize-0.7.0/taxize/man/fungorum.Rd |only taxize-0.7.0/taxize/man/gbif_downstream.Rd |only taxize-0.7.0/taxize/man/gbif_name_usage.Rd | 7 taxize-0.7.0/taxize/man/gbif_parse.Rd | 2 taxize-0.7.0/taxize/man/genbank2uid.Rd | 2 taxize-0.7.0/taxize/man/get_boldid.Rd | 2 taxize-0.7.0/taxize/man/get_colid.Rd | 2 taxize-0.7.0/taxize/man/get_eolid.Rd | 2 taxize-0.7.0/taxize/man/get_gbifid.Rd | 2 taxize-0.7.0/taxize/man/get_genes-deprecated.Rd | 2 taxize-0.7.0/taxize/man/get_genes_avail-deprecated.Rd | 2 taxize-0.7.0/taxize/man/get_ids.Rd | 7 taxize-0.7.0/taxize/man/get_nbnid.Rd | 2 taxize-0.7.0/taxize/man/get_seqs-deprecated.Rd | 2 taxize-0.7.0/taxize/man/get_tpsid.Rd | 2 taxize-0.7.0/taxize/man/get_tsn.Rd | 2 taxize-0.7.0/taxize/man/get_ubioid-defunct.Rd | 2 taxize-0.7.0/taxize/man/get_uid.Rd | 2 taxize-0.7.0/taxize/man/getacceptednamesfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getanymatchcount.Rd | 2 taxize-0.7.0/taxize/man/getcommentdetailfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getcommonnamesfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getcoremetadatafromtsn.Rd | 2 taxize-0.7.0/taxize/man/getcoveragefromtsn.Rd | 2 taxize-0.7.0/taxize/man/getcredibilityratingfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getcredibilityratings.Rd | 2 taxize-0.7.0/taxize/man/getcurrencyfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getdatedatafromtsn.Rd | 2 taxize-0.7.0/taxize/man/getdescription.Rd | 4 taxize-0.7.0/taxize/man/getexpertsfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getfullhierarchyfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getfullrecordfromlsid.Rd | 2 taxize-0.7.0/taxize/man/getfullrecordfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getgeographicdivisionsfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getgeographicvalues.Rd | 2 taxize-0.7.0/taxize/man/getglobalspeciescompletenessfromtsn.Rd | 2 taxize-0.7.0/taxize/man/gethierarchydownfromtsn.Rd | 2 taxize-0.7.0/taxize/man/gethierarchyupfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getitisterms.Rd | 2 taxize-0.7.0/taxize/man/getitistermsfromcommonname.Rd | 2 taxize-0.7.0/taxize/man/getitistermsfromscientificname.Rd | 2 taxize-0.7.0/taxize/man/getjurisdictionaloriginfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getjurisdictionoriginvalues.Rd | 2 taxize-0.7.0/taxize/man/getjurisdictionvalues.Rd | 2 taxize-0.7.0/taxize/man/getkey.Rd | 2 taxize-0.7.0/taxize/man/getkingdomnamefromtsn.Rd | 2 taxize-0.7.0/taxize/man/getkingdomnames.Rd | 2 taxize-0.7.0/taxize/man/getlastchangedate.Rd | 2 taxize-0.7.0/taxize/man/getlsidfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getothersourcesfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getparenttsnfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getpublicationsfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getranknames.Rd | 2 taxize-0.7.0/taxize/man/getrecordfromlsid.Rd | 4 taxize-0.7.0/taxize/man/getreviewyearfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getscientificnamefromtsn.Rd | 2 taxize-0.7.0/taxize/man/getsynonymnamesfromtsn.Rd | 2 taxize-0.7.0/taxize/man/gettaxonauthorshipfromtsn.Rd | 2 taxize-0.7.0/taxize/man/gettaxonomicranknamefromtsn.Rd | 2 taxize-0.7.0/taxize/man/gettaxonomicusagefromtsn.Rd | 2 taxize-0.7.0/taxize/man/gettsnbyvernacularlanguage.Rd | 2 taxize-0.7.0/taxize/man/gettsnfromlsid.Rd | 2 taxize-0.7.0/taxize/man/getunacceptabilityreasonfromtsn.Rd | 2 taxize-0.7.0/taxize/man/getvernacularlanguages.Rd | 2 taxize-0.7.0/taxize/man/gisd_invasive-defunct.Rd | 2 taxize-0.7.0/taxize/man/gni_details.Rd | 2 taxize-0.7.0/taxize/man/gni_parse.Rd | 2 taxize-0.7.0/taxize/man/gni_search.Rd | 2 taxize-0.7.0/taxize/man/gnr_datasources.Rd | 2 taxize-0.7.0/taxize/man/gnr_resolve.Rd | 17 taxize-0.7.0/taxize/man/ion.Rd |only taxize-0.7.0/taxize/man/iplant_resolve.Rd | 2 taxize-0.7.0/taxize/man/ipni_search.Rd | 2 taxize-0.7.0/taxize/man/itis-api.Rd | 2 taxize-0.7.0/taxize/man/itis_acceptname.Rd | 2 taxize-0.7.0/taxize/man/itis_downstream.Rd | 2 taxize-0.7.0/taxize/man/itis_getrecord.Rd | 2 taxize-0.7.0/taxize/man/itis_hierarchy.Rd | 2 taxize-0.7.0/taxize/man/itis_kingdomnames.Rd | 2 taxize-0.7.0/taxize/man/itis_lsid.Rd | 2 taxize-0.7.0/taxize/man/itis_name-deprecated.Rd | 2 taxize-0.7.0/taxize/man/itis_native.Rd | 2 taxize-0.7.0/taxize/man/itis_refs.Rd | 2 taxize-0.7.0/taxize/man/itis_searchcommon.Rd | 2 taxize-0.7.0/taxize/man/itis_taxrank.Rd | 2 taxize-0.7.0/taxize/man/itis_terms.Rd | 2 taxize-0.7.0/taxize/man/iucn_getname.Rd | 20 taxize-0.7.0/taxize/man/iucn_id.Rd | 13 taxize-0.7.0/taxize/man/iucn_status.Rd | 2 taxize-0.7.0/taxize/man/iucn_summary.Rd | 11 taxize-0.7.0/taxize/man/names_list.Rd | 2 taxize-0.7.0/taxize/man/nbn_classification.Rd | 2 taxize-0.7.0/taxize/man/nbn_search.Rd | 2 taxize-0.7.0/taxize/man/nbn_synonyms.Rd | 2 taxize-0.7.0/taxize/man/ncbi_children.Rd | 2 taxize-0.7.0/taxize/man/ncbi_get_taxon_summary.Rd | 2 taxize-0.7.0/taxize/man/ncbi_getbyid-defunct.Rd | 2 taxize-0.7.0/taxize/man/ncbi_getbyname-defunct.Rd | 6 taxize-0.7.0/taxize/man/ncbi_search-defunct.Rd | 6 taxize-0.7.0/taxize/man/phylomatic_format-defunct.Rd |only taxize-0.7.0/taxize/man/phylomatic_tree-defunct.Rd |only taxize-0.7.0/taxize/man/ping.Rd | 5 taxize-0.7.0/taxize/man/plantGenusNames.Rd | 2 taxize-0.7.0/taxize/man/plantNames.Rd | 2 taxize-0.7.0/taxize/man/plantminer.Rd | 2 taxize-0.7.0/taxize/man/rank_ref.Rd | 2 taxize-0.7.0/taxize/man/rankagg.Rd | 2 taxize-0.7.0/taxize/man/resolve.Rd | 7 taxize-0.7.0/taxize/man/sci2comm.Rd | 8 taxize-0.7.0/taxize/man/scrapenames.Rd | 2 taxize-0.7.0/taxize/man/searchbycommonname.Rd | 8 taxize-0.7.0/taxize/man/searchbycommonnamebeginswith.Rd | 2 taxize-0.7.0/taxize/man/searchbycommonnameendswith.Rd | 2 taxize-0.7.0/taxize/man/searchbyscientificname.Rd | 2 taxize-0.7.0/taxize/man/searchforanymatch.Rd | 2 taxize-0.7.0/taxize/man/searchforanymatchpaged.Rd | 2 taxize-0.7.0/taxize/man/status_codes.Rd | 2 taxize-0.7.0/taxize/man/synonyms.Rd | 6 taxize-0.7.0/taxize/man/tax_agg.Rd | 7 taxize-0.7.0/taxize/man/tax_name.Rd | 2 taxize-0.7.0/taxize/man/tax_rank.Rd | 6 taxize-0.7.0/taxize/man/taxize-defunct.Rd | 6 taxize-0.7.0/taxize/man/taxize-package.Rd | 18 taxize-0.7.0/taxize/man/taxize_capwords.Rd | 2 taxize-0.7.0/taxize/man/taxize_cite.Rd | 2 taxize-0.7.0/taxize/man/taxize_ldfast.Rd | 2 taxize-0.7.0/taxize/man/theplantlist.Rd | 9 taxize-0.7.0/taxize/man/tnrs.Rd | 2 taxize-0.7.0/taxize/man/tnrs_sources.Rd | 2 taxize-0.7.0/taxize/man/tp_acceptednames-deprecated.Rd | 2 taxize-0.7.0/taxize/man/tp_accnames.Rd | 2 taxize-0.7.0/taxize/man/tp_classification-defunct.Rd | 2 taxize-0.7.0/taxize/man/tp_dist.Rd | 2 taxize-0.7.0/taxize/man/tp_namedistributions-deprecated.Rd | 2 taxize-0.7.0/taxize/man/tp_namereferences-deprecated.Rd | 2 taxize-0.7.0/taxize/man/tp_refs.Rd | 2 taxize-0.7.0/taxize/man/tp_search.Rd | 2 taxize-0.7.0/taxize/man/tp_summary.Rd | 2 taxize-0.7.0/taxize/man/tp_synonyms.Rd | 2 taxize-0.7.0/taxize/man/tpl_families.Rd | 2 taxize-0.7.0/taxize/man/tpl_get.Rd | 2 taxize-0.7.0/taxize/man/tpl_search-defunct.Rd | 2 taxize-0.7.0/taxize/man/ubio_classification-defunct.Rd | 2 taxize-0.7.0/taxize/man/ubio_classification_search-defunct.Rd | 2 taxize-0.7.0/taxize/man/ubio_id-defunct.Rd | 2 taxize-0.7.0/taxize/man/ubio_ping-defunct.Rd | 2 taxize-0.7.0/taxize/man/ubio_search-defunct.Rd | 2 taxize-0.7.0/taxize/man/ubio_synonyms-defunct.Rd | 2 taxize-0.7.0/taxize/man/upstream.Rd | 7 taxize-0.7.0/taxize/man/vascan_search.Rd | 2 taxize-0.7.0/taxize/tests/testthat/Rplots.pdf |binary taxize-0.7.0/taxize/tests/testthat/test-apgscraping.R | 32 taxize-0.7.0/taxize/tests/testthat/test-classification.R | 7 taxize-0.7.0/taxize/tests/testthat/test-col_children.R | 41 taxize-0.7.0/taxize/tests/testthat/test-col_downstream.R | 21 taxize-0.7.0/taxize/tests/testthat/test-downstream.R |only taxize-0.7.0/taxize/tests/testthat/test-eubon.R |only taxize-0.7.0/taxize/tests/testthat/test-fungorum.R |only taxize-0.7.0/taxize/tests/testthat/test-gbif_downstream.R |only taxize-0.7.0/taxize/tests/testthat/test-ion.R |only taxize-0.7.0/taxize/tests/testthat/test-ipni_search.R | 10 taxize-0.7.0/taxize/tests/testthat/test-itis_downstream.R | 4 taxize-0.7.0/taxize/tests/testthat/test-iucn_getname.R | 6 taxize-0.7.0/taxize/tests/testthat/test-iucn_id.R | 3 taxize-0.7.0/taxize/tests/testthat/test-iucn_summary.R | 2 taxize-0.7.0/taxize/tests/testthat/test-ping.R | 7 taxize-0.7.0/taxize/tests/testthat/test-tax_name.R | 8 taxize-0.7.0/taxize/vignettes/taxize_infotable.Rmd | 2 taxize-0.7.0/taxize/vignettes/taxize_vignette.Rmd | 14 247 files changed, 894 insertions(+), 900 deletions(-)
Title: Penalized Ordinal Regression
Description: Fits ordinal regression models with elastic net penalty.
Supported models include cumulative logit, probit, cauchit, and complementary log-log.
The algorithm uses Fisher Scoring with Coordinate Descent updates.
Author: Mike Wurm [aut, cre]
Maintainer: Mike Wurm <wurm@wisc.edu>
Diff between ordinalNet versions 1.2 dated 2015-11-25 and 1.3 dated 2015-11-30
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- tests/testthat.R | 4 ++-- tests/testthat/test-ordinalNet.R | 30 +++++++++++++++++++++--------- 4 files changed, 30 insertions(+), 18 deletions(-)
Title: Model Implied Instrumental Variable (MIIV) Estimation of
Structural Equation Models
Description: Functions for estimating structural equation models using model-
implied instrumental variables.
Author: Zachary Fisher, Ken Bollen and Kathleen Gates.
Maintainer: Zachary Fisher <fish.zachary@gmail.com>
Diff between MIIVsem versions 0.4.3 dated 2015-11-15 and 0.4.4 dated 2015-11-30
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/miive.R | 20 +++++++++++--------- 3 files changed, 16 insertions(+), 14 deletions(-)
Title: Alignment of Phonetic Sequences Using the 'ALINE' Algorithm
Description: Functions are provided to calculate the 'ALINE' Distance between words. The score is based on phonetic features represented using the Unicode-compliant International Phonetic Alphabet (IPA). Parameterized features weights are used to determine the optimal alignment and functions are provided to estimate optimum values.
Author: Sean Downey [aut, cre],
Guowei Sun [aut]
Maintainer: Sean Downey <sdowney2@umd.edu>
Diff between alineR versions 1.1.1 dated 2015-08-06 and 1.1.2 dated 2015-11-30
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NAMESPACE | 2 +- R/features.plot.R | 32 ++++++++++++++++---------------- man/features.plot.Rd | 8 +++++++- src/Word.cpp | 3 ++- src/Word.h | 3 +-- 7 files changed, 36 insertions(+), 30 deletions(-)
Title: Tools for Spatial Data Analysis
Description: Tools for spatial data analysis. Emphasis on kriging. Provides functions for prediction and simulation. Intended to be relatively straightforward, fast, and flexible.
Author: Joshua French <joshua.french@ucdenver.edu>
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Diff between SpatialTools versions 1.0.0 dated 2015-10-01 and 1.0.1 dated 2015-11-30
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 2 ++ R/krige_tools.R | 3 +++ man/krige.ok.Rd | 7 ++++--- man/krige.sk.Rd | 13 +++++++------ man/krige.uk.Rd | 4 +++- 7 files changed, 29 insertions(+), 20 deletions(-)
Title: Neo4j Driver for R
Description: Neo4j, a graph database, allows users to store their data as a property graph. A graph consists of nodes that are connected by relationships; both nodes and relationships can have properties, or key-value pairs. RNeo4j is Neo4j's R driver. It allows users to read and write data from and to Neo4j directly from their R environment by exposing an interface for interacting with nodes, relationships, paths, and more. Most notably, it allows users to retrieve Cypher query results as R data frames, where Cypher is Neo4j's graph query language. Visit <http://www.neo4j.com> to learn more about Neo4j.
Author: Nicole White
Maintainer: Nicole White <nicole@neo4j.com>
Diff between RNeo4j versions 1.6.0 dated 2015-10-11 and 1.6.1 dated 2015-11-30
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/getConstraint.R | 38 +++++++++++--------------------------- R/getIndex.R | 51 +++++++++++---------------------------------------- R/internal.R | 2 +- 5 files changed, 30 insertions(+), 75 deletions(-)
Title: Multivariate Data Analysis for Chemometrics
Description: Package implements projection based methods for preprocessing,
exploring and analysis of multivariate data used in chemometrics.
Author: Sergey Kucheryavskiy
Maintainer: Sergey Kucheryavskiy <svkucheryavski@gmail.com>
Diff between mdatools versions 0.6.0 dated 2015-01-19 and 0.7.0 dated 2015-11-30
DESCRIPTION | 17 - MD5 | 500 ++++++++++++++++----------------- NAMESPACE | 212 +++++++++++++ NEWS | 22 + R/classmodel.R | 8 R/classres.R | 102 ++++-- R/crossval.R | 36 ++ R/defaults.R | 69 ++++ R/ipls.R |only R/ldecomp.R | 93 +++--- R/mdaplots.R | 455 +++++++++++++++++++++++------- R/pca.R | 271 +++++++++++++---- R/pcares.R | 125 +++++++- R/pls.R | 494 ++++++++++++++++++++++++++++---- R/plsda.R | 260 ++++++++++++++--- R/plsdares.R | 151 ++++++++- R/plsres.R | 169 +++++++++-- R/prep.R | 40 ++ R/randtest.R | 126 ++++++-- R/regcoeffs.R | 13 R/regres.R | 19 - R/simca.R | 198 +++++++++---- R/simcam.R | 154 ++++++++-- R/simcamres.R | 166 ++++++++-- R/simcares.R | 117 ++++++- README.md | 13 man/as.matrix.classres.Rd | 2 man/as.matrix.ldecomp.Rd | 2 man/as.matrix.plsdares.Rd | 2 man/as.matrix.plsres.Rd | 2 man/as.matrix.regcoeffs.Rd | 2 man/as.matrix.regres.Rd | 2 man/bars.Rd | 6 man/classify.plsda.Rd | 2 man/classres.Rd | 57 +-- man/crossval.Rd | 2 man/crossval.str.Rd |only man/erfinv.Rd | 2 man/errorbars.Rd | 2 man/getCalibrationData.Rd | 2 man/getCalibrationData.pca.Rd | 2 man/getCalibrationData.simcam.Rd | 2 man/getClassificationPerformance.Rd | 2 man/getMainTitle.Rd | 2 man/getRegcoeffs.Rd |only man/getRegcoeffs.pls.Rd |only man/getSelectedComponents.Rd | 2 man/getSelectedComponents.classres.Rd | 2 man/getSelectivityRatio.Rd | 2 man/getSelectivityRatio.pls.Rd | 2 man/getVIPScores.Rd | 2 man/getVIPScores.pls.Rd | 2 man/ipls.Rd |only man/ipls.backward.Rd |only man/ipls.forward.Rd |only man/ldecomp.Rd | 8 man/ldecomp.getDistances.Rd | 9 man/ldecomp.getResLimits.Rd | 8 man/ldecomp.getVariances.Rd | 6 man/mdaplot.Rd | 156 ++++++---- man/mdaplot.areColors.Rd | 2 man/mdaplot.formatValues.Rd | 2 man/mdaplot.getAxesLim.Rd | 2 man/mdaplot.getColors.Rd | 2 man/mdaplot.plotAxes.Rd | 2 man/mdaplot.showColorbar.Rd | 2 man/mdaplot.showGrid.Rd | 2 man/mdaplot.showLabels.Rd | 2 man/mdaplot.showLegend.Rd | 8 man/mdaplot.showLines.Rd | 2 man/mdaplot.showRegressionLine.Rd | 2 man/mdaplotg.Rd | 131 +++++--- man/mdatools.Rd | 2 man/pca.Rd | 132 ++++---- man/pca.cal.Rd | 2 man/pca.crossval.Rd | 2 man/pca.mvreplace.Rd | 66 ++-- man/pca.nipals.Rd | 7 man/pca.svd.Rd | 2 man/pcares.Rd | 87 ++--- man/pinv.Rd | 2 man/plot.classres.Rd | 2 man/plot.ipls.Rd |only man/plot.pca.Rd | 2 man/plot.pcares.Rd | 4 man/plot.pls.Rd | 2 man/plot.plsda.Rd | 6 man/plot.plsdares.Rd | 7 man/plot.plsres.Rd | 2 man/plot.randtest.Rd | 2 man/plot.regcoeffs.Rd | 4 man/plot.regres.Rd | 2 man/plot.simca.Rd | 2 man/plot.simcam.Rd | 2 man/plot.simcamres.Rd | 2 man/plotCooman.Rd | 2 man/plotCooman.simcam.Rd | 2 man/plotCooman.simcamres.Rd | 2 man/plotCorr.Rd | 2 man/plotCorr.randtest.Rd | 2 man/plotCumVariance.Rd | 2 man/plotCumVariance.ldecomp.Rd | 2 man/plotCumVariance.pca.Rd | 2 man/plotDiscriminationPower.Rd | 2 man/plotDiscriminationPower.simcam.Rd | 2 man/plotHist.Rd | 2 man/plotHist.randtest.Rd | 2 man/plotLoadings.Rd | 2 man/plotLoadings.pca.Rd | 2 man/plotMisclassified.Rd | 2 man/plotMisclassified.classmodel.Rd | 2 man/plotMisclassified.classres.Rd | 2 man/plotModelDistance.Rd | 2 man/plotModelDistance.simcam.Rd | 2 man/plotModellingPower.Rd | 2 man/plotModellingPower.simca.Rd | 2 man/plotModellingPower.simcam.Rd | 2 man/plotPerformance.Rd | 2 man/plotPerformance.classmodel.Rd | 2 man/plotPerformance.classres.Rd | 2 man/plotPredictions.Rd | 2 man/plotPredictions.classmodel.Rd | 2 man/plotPredictions.classres.Rd | 2 man/plotPredictions.pls.Rd | 2 man/plotPredictions.plsres.Rd | 2 man/plotPredictions.regres.Rd | 2 man/plotRMSE.Rd | 2 man/plotRMSE.ipls.Rd |only man/plotRMSE.pls.Rd | 2 man/plotRMSE.plsres.Rd | 2 man/plotRMSE.regres.Rd | 2 man/plotRegcoeffs.Rd | 2 man/plotRegcoeffs.pls.Rd | 6 man/plotResiduals.Rd | 2 man/plotResiduals.ldecomp.Rd | 7 man/plotResiduals.pca.Rd | 7 man/plotResiduals.simcam.Rd | 2 man/plotResiduals.simcamres.Rd | 8 man/plotResiduals.simcares.Rd | 8 man/plotScores.Rd | 2 man/plotScores.ldecomp.Rd | 2 man/plotScores.pca.Rd | 2 man/plotSelection.Rd |only man/plotSelection.ipls.Rd |only man/plotSelectivityRatio.Rd | 2 man/plotSelectivityRatio.pls.Rd | 2 man/plotSensitivity.Rd | 2 man/plotSensitivity.classmodel.Rd | 2 man/plotSensitivity.classres.Rd | 2 man/plotSpecificity.Rd | 2 man/plotSpecificity.classmodel.Rd | 2 man/plotSpecificity.classres.Rd | 2 man/plotVIPScores.Rd | 2 man/plotVIPScores.pls.Rd | 2 man/plotVariance.Rd | 2 man/plotVariance.ldecomp.Rd | 2 man/plotVariance.pca.Rd | 2 man/plotVariance.pls.Rd | 2 man/plotXCumVariance.Rd | 2 man/plotXCumVariance.pls.Rd | 2 man/plotXCumVariance.plsres.Rd | 2 man/plotXLoadings.Rd | 2 man/plotXLoadings.pls.Rd | 2 man/plotXResiduals.Rd | 2 man/plotXResiduals.pls.Rd | 7 man/plotXResiduals.plsres.Rd | 4 man/plotXScores.Rd | 2 man/plotXScores.pls.Rd | 2 man/plotXScores.plsres.Rd | 2 man/plotXVariance.Rd | 2 man/plotXVariance.pls.Rd | 2 man/plotXVariance.plsres.Rd | 2 man/plotXYLoadings.Rd | 2 man/plotXYLoadings.pls.Rd | 2 man/plotXYScores.Rd | 2 man/plotXYScores.pls.Rd | 2 man/plotXYScores.plsres.Rd | 2 man/plotYCumVariance.Rd | 2 man/plotYCumVariance.pls.Rd | 2 man/plotYCumVariance.plsres.Rd | 2 man/plotYResiduals.Rd | 2 man/plotYResiduals.pls.Rd | 2 man/plotYResiduals.regres.Rd | 2 man/plotYVariance.Rd | 2 man/plotYVariance.pls.Rd | 2 man/plotYVariance.plsres.Rd | 2 man/pls.Rd | 204 +++++++------ man/pls.cal.Rd | 7 man/pls.calculateSelectivityRatio.Rd | 2 man/pls.calculateVIPScores.Rd | 2 man/pls.crossval.Rd | 2 man/pls.simpls.Rd | 2 man/plsda.Rd | 143 +++++---- man/plsda.crossval.Rd | 6 man/plsda.getReferenceValues.Rd | 2 man/plsdares.Rd | 124 +++----- man/plsres.Rd | 133 ++++---- man/predict.pca.Rd | 2 man/predict.pls.Rd | 2 man/predict.plsda.Rd | 2 man/predict.simca.Rd | 2 man/predict.simcam.Rd | 2 man/prep.autoscale.Rd | 2 man/prep.msc.Rd | 2 man/prep.norm.Rd |only man/prep.savgol.Rd | 2 man/prep.snv.Rd | 2 man/print.classres.Rd | 2 man/print.ipls.Rd |only man/print.ldecomp.Rd | 2 man/print.pca.Rd | 2 man/print.pcares.Rd | 2 man/print.pls.Rd | 2 man/print.plsda.Rd | 2 man/print.plsdares.Rd | 2 man/print.plsres.Rd | 2 man/print.randtest.Rd | 2 man/print.regcoeffs.Rd | 2 man/print.regres.Rd | 2 man/print.simca.Rd | 2 man/print.simcam.Rd | 2 man/print.simcamres.Rd | 2 man/print.simcares.Rd | 2 man/randtest.Rd | 104 +++--- man/regcoeffs.Rd | 2 man/regcoeffs.getStat.Rd | 2 man/regres.Rd | 2 man/regres.bias.Rd | 2 man/regres.r2.Rd | 2 man/regres.rmse.Rd | 2 man/regres.slope.Rd | 2 man/selectCompNum.Rd | 2 man/selectCompNum.pca.Rd | 2 man/selectCompNum.pls.Rd | 5 man/showPredictions.Rd | 2 man/showPredictions.classres.Rd | 2 man/simca.Rd | 160 +++++----- man/simca.classify.Rd | 4 man/simca.crossval.Rd | 2 man/simcam.Rd | 112 +++---- man/simcam.getPerformanceStatistics.Rd | 2 man/simcamres.Rd | 94 ++---- man/simcares.Rd | 93 ++---- man/summary.classres.Rd | 2 man/summary.ipls.Rd |only man/summary.ldecomp.Rd | 2 man/summary.pca.Rd | 2 man/summary.pcares.Rd | 2 man/summary.pls.Rd | 2 man/summary.plsda.Rd | 2 man/summary.plsdares.Rd | 2 man/summary.plsres.Rd | 2 man/summary.randtest.Rd | 2 man/summary.regres.Rd | 2 man/summary.simca.Rd | 2 man/summary.simcam.Rd | 2 man/summary.simcamres.Rd | 2 man/summary.simcares.Rd | 2 258 files changed, 4211 insertions(+), 1921 deletions(-)
Title: Use LaTeX Expressions in Plots
Description: Parses and converts LaTeX math formulas to R's plotmath
expressions, used to enter mathematical formulas and symbols to be rendered as
text, axis labels, etc. throughout R's plotting system.
Author: Stefano Meschiari [aut, cre]
Maintainer: Stefano Meschiari <stefano.meschiari@gmail.com>
Diff between latex2exp versions 0.3.3 dated 2015-08-12 and 0.4.0 dated 2015-11-30
latex2exp-0.3.3/latex2exp/inst/doc/latex2exp.R |only latex2exp-0.3.3/latex2exp/inst/doc/latex2exp.Rmd |only latex2exp-0.3.3/latex2exp/inst/doc/latex2exp.html |only latex2exp-0.3.3/latex2exp/tests/testthat/Rplots.pdf |only latex2exp-0.3.3/latex2exp/vignettes/latex2exp.Rmd |only latex2exp-0.4.0/latex2exp/DESCRIPTION | 15 +++-- latex2exp-0.4.0/latex2exp/MD5 | 30 +++++------ latex2exp-0.4.0/latex2exp/NAMESPACE | 1 latex2exp-0.4.0/latex2exp/R/latex2exp.R | 42 ++++++++++------ latex2exp-0.4.0/latex2exp/build/vignette.rds |binary latex2exp-0.4.0/latex2exp/inst/doc/using-latex2exp.R |only latex2exp-0.4.0/latex2exp/inst/doc/using-latex2exp.Rmd |only latex2exp-0.4.0/latex2exp/inst/doc/using-latex2exp.html |only latex2exp-0.4.0/latex2exp/man/TeX.Rd |only latex2exp-0.4.0/latex2exp/man/latex2exp.Rd | 13 +--- latex2exp-0.4.0/latex2exp/man/latex2exp_examples.Rd | 6 +- latex2exp-0.4.0/latex2exp/man/latex2exp_supported.Rd | 2 latex2exp-0.4.0/latex2exp/man/plot.expression.Rd | 2 latex2exp-0.4.0/latex2exp/man/print.latextoken.Rd | 6 +- latex2exp-0.4.0/latex2exp/man/toString.latextoken.Rd | 8 +-- latex2exp-0.4.0/latex2exp/vignettes/using-latex2exp.Rmd |only 21 files changed, 68 insertions(+), 57 deletions(-)
Title: Convert Statistical Analysis Objects into Tidy Data Frames
Description: Convert statistical analysis objects from R into tidy data frames,
so that they can more easily be combined, reshaped and otherwise processed
with tools like 'dplyr', 'tidyr' and 'ggplot2'. The package provides three S3
generics: tidy, which summarizes a model's statistical findings such as
coefficients of a regression; augment, which adds columns to the original
data such as predictions, residuals and cluster assignments; and glance,
which provides a one-row summary of model-level statistics.
Author: David Robinson [aut, cre],
Matthieu Gomez [ctb],
Boris Demeshev [ctb],
Dieter Menne [ctb],
Benjamin Nutter [ctb],
Luke Johnston [ctb],
Ben Bolker [ctb],
Francois Briatte [ctb],
Hadley Wickham [ctb]
Maintainer: David Robinson <admiral.david@gmail.com>
Diff between broom versions 0.3.7 dated 2015-05-06 and 0.4.0 dated 2015-11-30
DESCRIPTION | 24 ++- MD5 | 148 +++++++++++++-------- NAMESPACE | 49 +++++++ R/anova_tidiers.R | 35 ++++- R/arima_tidiers.R | 2 R/auc_tidiers.R |only R/augment.R | 13 + R/biglm_tidiers.R | 10 + R/bingroup_tidiers.R |only R/boot_tidiers.R |only R/broom.R | 5 R/btergm_tidiers.R |only R/data.frame_tidiers.R | 2 R/ergm_tidiers.R |only R/felm_tidiers.R | 18 +- R/fitdistr_tidiers.R |only R/gamlss_tidiers.R |only R/geeglm_tidiers.R |only R/glmnet_tidiers.R | 18 +- R/globals.R | 4 R/htest_tidiers.R | 14 ++ R/list_tidiers.R | 19 ++ R/lm_tidiers.R | 28 ++-- R/lme4_tidiers.R | 194 +++++++++++++++++++++++----- R/loess_tidiers.R | 2 R/map_tidiers.R | 2 R/mcmc_tidiers.R |only R/mle2_tidiers.R |only R/multcomp_tidiers.R | 2 R/multinom_tidiers.R | 15 +- R/nlme_tidiers.R | 4 R/nls_tidiers.R | 21 ++- R/plm_tidiers.R | 2 R/psych_tidiers.R |only R/rcorr_tidiers.R |only R/ridgelm_tidiers.R | 13 + R/rowwise_df_tidiers.R | 75 +++++++++-- R/rq_tidiers.R |only R/smooth.spline_tidiers.R | 4 R/stats_tidiers.R | 4 R/summary_tidiers.R | 12 + R/survival_tidiers.R | 30 ++-- R/svd_tidiers.R |only R/utilities.R | 38 ++--- R/xyz_tidiers.R |only README.md | 283 ++++++++++++++++++++++++++++-------------- build/vignette.rds |binary inst/doc/bootstrapping.Rmd | 2 inst/doc/bootstrapping.html | 46 +++--- inst/doc/broom_and_dplyr.html | 158 ++++++++++++----------- inst/doc/kmeans.html | 8 - inst/extdata |only man/auc_tidiers.Rd |only man/augment.Rd | 10 - man/biglm_tidiers.Rd | 5 man/binDesign_tidiers.Rd |only man/binWidth_tidiers.Rd |only man/boot_tidiers.Rd |only man/btergm_tidiers.Rd |only man/cch_tidiers.Rd | 4 man/confint.geeglm.Rd |only man/confint_tidy.Rd | 4 man/coxph_tidiers.Rd | 2 man/ergm_tidiers.Rd |only man/fitdistr_tidiers.Rd |only man/gamlss_tidiers.Rd |only man/geeglm_tidiers.Rd |only man/kappa_tidiers.Rd |only man/list_tidiers.Rd | 8 - man/lm_tidiers.Rd | 14 +- man/lme4_tidiers.Rd | 39 +++-- man/loess_tidiers.Rd | 2 man/mcmc_tidiers.Rd |only man/mle2_tidiers.Rd |only man/nls_tidiers.Rd | 6 man/plm_tidiers.Rd | 2 man/process_ergm.Rd |only man/process_geeglm.Rd |only man/process_rq.Rd |only man/rcorr_tidiers.Rd |only man/ridgelm_tidiers.Rd | 5 man/rowwise_df_tidiers.Rd | 43 ++++-- man/rq_tidiers.Rd |only man/summary_tidiers.Rd | 4 man/survreg_tidiers.Rd | 4 man/svd_tidiers.Rd |only man/xyz_tidiers.Rd |only tests/testthat/test-dplyr.R | 2 tests/testthat/test-lme4.R | 24 +++ tests/testthat/test-nlme.R | 61 ++++----- tests/testthat/test-rowwise.R |only tests/testthat/test-tidy.R | 12 + vignettes/bootstrapping.Rmd | 2 93 files changed, 1065 insertions(+), 492 deletions(-)
Title: Matrices Backed by Binary PED Files (PLINK)
Description: A matrix-like data structure that allows for efficient,
convenient, and scalable subsetting of binary genotype/phenotype files
generated by PLINK (http://pngu.mgh.harvard.edu/~purcell/plink/), the whole
genome association analysis toolset, without loading the entire file into
memory.
Author: Alexander Grueneberg [aut, cre],
Lian Lian [ctb],
Gustavo de los Campos [ctb]
Maintainer: Alexander Grueneberg <alexander.grueneberg@googlemail.com>
Diff between BEDMatrix versions 1.0.1 dated 2015-11-12 and 1.1.0 dated 2015-11-30
BEDMatrix-1.0.1/BEDMatrix/cleanup |only BEDMatrix-1.0.1/BEDMatrix/configure |only BEDMatrix-1.0.1/BEDMatrix/configure.ac |only BEDMatrix-1.0.1/BEDMatrix/src/Makevars.in |only BEDMatrix-1.0.1/BEDMatrix/tools |only BEDMatrix-1.1.0/BEDMatrix/DESCRIPTION | 11 +++++------ BEDMatrix-1.1.0/BEDMatrix/MD5 | 18 +++++------------- BEDMatrix-1.1.0/BEDMatrix/README.md | 10 ---------- BEDMatrix-1.1.0/BEDMatrix/src/BEDMatrix.cpp | 21 ++++++++++++++------- BEDMatrix-1.1.0/BEDMatrix/src/Makevars |only BEDMatrix-1.1.0/BEDMatrix/src/Makevars.win |only 11 files changed, 24 insertions(+), 36 deletions(-)
Title: A Toolbox for Writing Pretty Papers and Reports
Description: A toolbox for writing 'knitr', 'Sweave' or other 'LaTeX'- or 'markdown'-based
reports and to prettify the output of various estimated models.
Author: Benjamin Hofner, with contributions by many others (see inst/CONTRIBUTIONS)
Maintainer: Benjamin Hofner <benjamin.hofner@fau.de>
Diff between papeR versions 0.6-1 dated 2015-06-09 and 1.0-0 dated 2015-11-30
papeR-0.6-1/papeR/R/latex_table.R |only papeR-0.6-1/papeR/tests/regtest-prettify.R |only papeR-1.0-0/papeR/ChangeLog | 492 +++++++++++++++++++++++++++- papeR-1.0-0/papeR/DESCRIPTION | 21 - papeR-1.0-0/papeR/MD5 | 58 ++- papeR-1.0-0/papeR/NAMESPACE | 48 +- papeR-1.0-0/papeR/R/helpers.R | 41 +- papeR-1.0-0/papeR/R/labels.R | 199 +++-------- papeR-1.0-0/papeR/R/plot.R | 20 - papeR-1.0-0/papeR/R/prettify.R | 127 ++++--- papeR-1.0-0/papeR/R/summarize.R |only papeR-1.0-0/papeR/R/toLatex.R | 25 - papeR-1.0-0/papeR/README.md |only papeR-1.0-0/papeR/build |only papeR-1.0-0/papeR/inst/CITATION | 6 papeR-1.0-0/papeR/inst/NEWS.Rd | 37 +- papeR-1.0-0/papeR/inst/SPSS |only papeR-1.0-0/papeR/inst/doc |only papeR-1.0-0/papeR/man/get_options.Rd | 6 papeR-1.0-0/papeR/man/labels.data.frame.Rd | 104 ++--- papeR-1.0-0/papeR/man/latex_table_cont.Rd | 159 +-------- papeR-1.0-0/papeR/man/latex_table_fac.Rd | 134 +------ papeR-1.0-0/papeR/man/papeR-package.Rd | 18 - papeR-1.0-0/papeR/man/summarize.Rd |only papeR-1.0-0/papeR/man/summarize_factor.Rd |only papeR-1.0-0/papeR/man/summarize_numeric.Rd |only papeR-1.0-0/papeR/man/toLatex.Rd | 8 papeR-1.0-0/papeR/man/xtable_summary.Rd |only papeR-1.0-0/papeR/tests/regtest-plot.R |only papeR-1.0-0/papeR/tests/regtest-summarize.R |only papeR-1.0-0/papeR/tests/testthat |only papeR-1.0-0/papeR/tests/testthat.R |only papeR-1.0-0/papeR/vignettes |only 33 files changed, 910 insertions(+), 593 deletions(-)
Title: Streamline Bioacoustic Analysis
Description: Offers three overarching categories of functions to obtain bird vocalization recordings from the web, manage sound files, and facilitate (bio)acoustic analysis in R.
Author: Marcelo Araya-Salas, Grace Smith Vidaurre, Hua Zhong
Maintainer: Marcelo Araya-Salas <marceloa27@gmail.com>
Diff between warbleR versions 1.0.3 dated 2015-09-09 and 1.1.0 dated 2015-11-30
warbleR-1.0.3/warbleR/vignettes/Phae.ad.csv |only warbleR-1.1.0/warbleR/DESCRIPTION | 10 warbleR-1.1.0/warbleR/MD5 | 92 +- warbleR-1.1.0/warbleR/NAMESPACE | 8 warbleR-1.1.0/warbleR/R/autodetec.R | 99 +- warbleR-1.1.0/warbleR/R/checkwavs.R | 5 warbleR-1.1.0/warbleR/R/coor.graph.R |only warbleR-1.1.0/warbleR/R/coor.sing-data.R |only warbleR-1.1.0/warbleR/R/coor.test.R |only warbleR-1.1.0/warbleR/R/dfts.R |only warbleR-1.1.0/warbleR/R/imp.raven.R |only warbleR-1.1.0/warbleR/R/imp.syrinx.R |only warbleR-1.1.0/warbleR/R/lspec.R | 17 warbleR-1.1.0/warbleR/R/manualoc.R | 10 warbleR-1.1.0/warbleR/R/mp32wav.R | 26 warbleR-1.1.0/warbleR/R/querxc.R | 36 warbleR-1.1.0/warbleR/R/selection.files-data.R |only warbleR-1.1.0/warbleR/R/sig2noise.R | 26 warbleR-1.1.0/warbleR/R/sim.coor.sing-data.R |only warbleR-1.1.0/warbleR/R/snrspecs.R | 19 warbleR-1.1.0/warbleR/R/specan.R | 21 warbleR-1.1.0/warbleR/R/specreator.R | 26 warbleR-1.1.0/warbleR/R/trackfreqs.R | 31 warbleR-1.1.0/warbleR/R/warbleR-package.R | 27 warbleR-1.1.0/warbleR/R/xcmaps.R | 124 ++- warbleR-1.1.0/warbleR/R/xcorr.R |only warbleR-1.1.0/warbleR/R/xcorr.graph.R |only warbleR-1.1.0/warbleR/R/zzz.R |only warbleR-1.1.0/warbleR/data/coor.sing.rda |only warbleR-1.1.0/warbleR/data/selection.files.rda |only warbleR-1.1.0/warbleR/data/sim.coor.sing.rda |only warbleR-1.1.0/warbleR/inst/CITATION | 5 warbleR-1.1.0/warbleR/inst/doc/warbleR_workflow.R | 22 warbleR-1.1.0/warbleR/inst/doc/warbleR_workflow.Rmd | 35 warbleR-1.1.0/warbleR/inst/doc/warbleR_workflow.html | 628 ++++++++-------- warbleR-1.1.0/warbleR/man/autodetec.Rd | 31 warbleR-1.1.0/warbleR/man/checkwavs.Rd | 5 warbleR-1.1.0/warbleR/man/coor.graph.Rd |only warbleR-1.1.0/warbleR/man/coor.sing.Rd |only warbleR-1.1.0/warbleR/man/coor.test.Rd |only warbleR-1.1.0/warbleR/man/dfts.Rd |only warbleR-1.1.0/warbleR/man/imp.raven.Rd |only warbleR-1.1.0/warbleR/man/imp.syrinx.Rd |only warbleR-1.1.0/warbleR/man/lspec.Rd | 6 warbleR-1.1.0/warbleR/man/mp32wav.Rd | 13 warbleR-1.1.0/warbleR/man/querxc.Rd | 18 warbleR-1.1.0/warbleR/man/selection.files.Rd |only warbleR-1.1.0/warbleR/man/sig2noise.Rd | 14 warbleR-1.1.0/warbleR/man/sim.coor.sing.Rd |only warbleR-1.1.0/warbleR/man/snrspecs.Rd | 10 warbleR-1.1.0/warbleR/man/specan.Rd | 6 warbleR-1.1.0/warbleR/man/specreator.Rd | 10 warbleR-1.1.0/warbleR/man/trackfreqs.Rd | 18 warbleR-1.1.0/warbleR/man/warbleR.Rd | 30 warbleR-1.1.0/warbleR/man/xcmaps.Rd | 14 warbleR-1.1.0/warbleR/man/xcorr.Rd |only warbleR-1.1.0/warbleR/man/xcorr.graph.Rd |only warbleR-1.1.0/warbleR/vignettes/Phae.snr.csv |only warbleR-1.1.0/warbleR/vignettes/acoustic_parameters.csv | 60 - warbleR-1.1.0/warbleR/vignettes/warbleR_workflow.Rmd | 35 60 files changed, 898 insertions(+), 639 deletions(-)
Title: Tools for Estimating Causal Dose Response Functions
Description: Functions and data to estimate causal dose response functions given continuous, ordinal, or binary treatments.
Author: Douglas Galagate [cre],
Joseph Schafer [aut]
Maintainer: Douglas Galagate <galagated@gmail.com>
Diff between causaldrf versions 0.2 dated 2015-10-17 and 0.3 dated 2015-11-30
DESCRIPTION | 16 +++++--- MD5 | 92 ++++++++++++++++++++++++++++++------------------- R/add_spl_est.R | 22 ++++++++++- R/aipwee_est.R | 40 +++++++++++++++++++-- R/bart_est.R | 37 ++++++++++++++++++- R/gam_est.R | 38 +++++++++++++++++--- R/hi_est.R | 72 +++++++++++++++++++++++++++++++++++--- R/hi_sim_data.R | 2 - R/iptw_est.R | 39 +++++++++++++++++++- R/ismw_est.R | 11 +++-- R/iw_est.R | 87 +++++++++++++++++++++++++++++++++++++++++++--- R/nw_est.R | 45 +++++++++++++++++++++-- R/overlap_fun.R | 38 ++++++++++++++------ R/prop_spline_est.R | 48 ++++++++++++++++--------- R/reg_est.R | 16 ++++++-- R/scalar_wts.R | 30 +++++++++++++++ R/sim_data.R | 2 - R/t_mod.R | 52 +++++++++++++++++++++++++++ R/wtrg_est.R | 8 +++- build |only inst |only man/add_spl_est.Rd | 10 ++++- man/aipwee_est.Rd | 33 +++++++++++++++++ man/bart_est.Rd | 34 +++++++++++++++++- man/gam_est.Rd | 22 +++++++++-- man/hi_est.Rd | 53 ++++++++++++++++++++++++++-- man/hi_sim_data.Rd | 2 - man/iptw_est.Rd | 19 +++++++++- man/ismw_est.Rd | 9 ++-- man/iw_est.Rd | 22 +++++++++-- man/nw_est.Rd | 14 +++++-- man/overlap_fun.Rd | 17 ++++----- man/prop_spline_est.Rd | 42 ++++++++++++++-------- man/reg_est.Rd | 10 ++++- man/scalar_wts.Rd | 2 + man/sim_data.Rd | 2 - man/t_mod.Rd | 2 + man/wtrg_est.Rd | 8 +++- vignettes |only 39 files changed, 827 insertions(+), 169 deletions(-)
Title: Analysing Inbreeding Based on Genetic Markers
Description: A framework for analysing inbreeding and heterozygosity-fitness
correlations (HFCs) based on microsatellite and SNP markers.
Author: Martin A. Stoffel [aut, cre],
Mareike Esser [aut]
Maintainer: Martin A. Stoffel <martin.adam.stoffel@gmail.com>
Diff between inbreedR versions 0.2.0 dated 2015-10-06 and 0.3.0 dated 2015-11-30
inbreedR-0.2.0/inbreedR/R/resample_g2.R |only inbreedR-0.2.0/inbreedR/man/resample_g2.Rd |only inbreedR-0.2.0/inbreedR/tests/testthat/test-resample-g2.R |only inbreedR-0.3.0/inbreedR/DESCRIPTION | 16 inbreedR-0.3.0/inbreedR/MD5 | 84 - inbreedR-0.3.0/inbreedR/NAMESPACE | 32 inbreedR-0.3.0/inbreedR/R/HHC.R | 144 +- inbreedR-0.3.0/inbreedR/R/check_data.R | 158 +- inbreedR-0.3.0/inbreedR/R/convert_raw.R | 118 +- inbreedR-0.3.0/inbreedR/R/g2_microsats.R | 337 ++--- inbreedR-0.3.0/inbreedR/R/g2_snps.R | 460 +++---- inbreedR-0.3.0/inbreedR/R/inbreedR.R | 128 +- inbreedR-0.3.0/inbreedR/R/mouse_msats.R | 30 inbreedR-0.3.0/inbreedR/R/mouse_snps.R | 32 inbreedR-0.3.0/inbreedR/R/plot.inbreed.R | 415 +++---- inbreedR-0.3.0/inbreedR/R/print.inbreed.R | 238 ++-- inbreedR-0.3.0/inbreedR/R/r2_Wf.R | 292 ++--- inbreedR-0.3.0/inbreedR/R/r2_hf.R | 454 +++---- inbreedR-0.3.0/inbreedR/R/sMLH.R | 151 +- inbreedR-0.3.0/inbreedR/R/simulate_g2.R |only inbreedR-0.3.0/inbreedR/R/simulate_r2_hf.R |only inbreedR-0.3.0/inbreedR/README.md | 86 - inbreedR-0.3.0/inbreedR/build/vignette.rds |binary inbreedR-0.3.0/inbreedR/inst/CITATION |only inbreedR-0.3.0/inbreedR/man/HHC.Rd | 83 - inbreedR-0.3.0/inbreedR/man/MLH.Rd |only inbreedR-0.3.0/inbreedR/man/bodyweight.Rd | 30 inbreedR-0.3.0/inbreedR/man/check_data.Rd | 88 - inbreedR-0.3.0/inbreedR/man/convert_raw.Rd | 67 - inbreedR-0.3.0/inbreedR/man/g2_microsats.Rd | 120 +- inbreedR-0.3.0/inbreedR/man/g2_snps.Rd | 135 +- inbreedR-0.3.0/inbreedR/man/inbreedR.Rd | 130 +- inbreedR-0.3.0/inbreedR/man/mouse_msats.Rd | 36 inbreedR-0.3.0/inbreedR/man/mouse_snps.Rd | 36 inbreedR-0.3.0/inbreedR/man/plot.inbreed.Rd | 60 - inbreedR-0.3.0/inbreedR/man/print.inbreed.Rd | 46 inbreedR-0.3.0/inbreedR/man/r2_Wf.Rd | 128 +- inbreedR-0.3.0/inbreedR/man/r2_hf.Rd | 127 +- inbreedR-0.3.0/inbreedR/man/sMLH.Rd | 69 - inbreedR-0.3.0/inbreedR/man/simulate_g2.Rd |only inbreedR-0.3.0/inbreedR/man/simulate_r2_hf.Rd |only inbreedR-0.3.0/inbreedR/tests/testthat/test-HHC.R | 2 inbreedR-0.3.0/inbreedR/tests/testthat/test-MLH.R |only inbreedR-0.3.0/inbreedR/tests/testthat/test-r2_Wf.R | 8 inbreedR-0.3.0/inbreedR/tests/testthat/test-r2_hf.R | 86 - inbreedR-0.3.0/inbreedR/tests/testthat/test-simulate_g2.R |only inbreedR-0.3.0/inbreedR/tests/testthat/test-simulate_r2_hf.R |only inbreedR-0.3.0/inbreedR/vignettes/bibliography.bib | 11 inbreedR-0.3.0/inbreedR/vignettes/inbreedR_step_by_step.Rmd | 635 +++++------ 49 files changed, 2615 insertions(+), 2457 deletions(-)
Title: R Interface to C API of IBM ILOG CPLEX
Description: This is the R Interface to the C API of IBM ILOG CPLEX. It necessarily depends on IBM ILOG CPLEX (>= 12.1).
Author: C. Jonathan Fritzemeier [cre, ctb], Gabriel Gelius-Dietrich [aut]
Maintainer: C. Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
Diff between cplexAPI versions 1.2.11 dated 2014-07-28 and 1.3.1 dated 2015-11-30
DESCRIPTION | 19 - LICENSE |only MD5 | 424 +++++++++++++++++----------------- README.md |only build/vignette.rds |binary inst/doc/cplexAPI.pdf |binary man/addChannelCPLEX.Rd | 5 man/addColsCPLEX.Rd | 5 man/addFpDestCPLEX.Rd | 5 man/addIndConstrCPLEX.Rd | 5 man/addMIPstartsCPLEX.Rd | 5 man/addQConstrCPLEX.Rd | 5 man/addRowsCPLEX.Rd | 5 man/baroptCPLEX.Rd | 5 man/baseWriteCPLEX.Rd | 5 man/basicPresolveCPLEX.Rd | 5 man/boundSaCPLEX.Rd | 5 man/cLpWriteCPLEX.Rd | 5 man/checkAddColsCPLEX.Rd | 5 man/checkAddRowsCPLEX.Rd | 5 man/checkChgCoefListCPLEX.Rd | 5 man/checkCopyColTypeCPLEX.Rd | 5 man/checkCopyLpCPLEX.Rd | 5 man/checkCopyLpwNamesCPLEX.Rd | 5 man/checkCopyQPsepCPLEX.Rd | 5 man/checkCopyQuadCPLEX.Rd | 5 man/checkValsCPLEX.Rd | 5 man/chgBndsCPLEX.Rd | 5 man/chgCoefCPLEX.Rd | 5 man/chgCoefListCPLEX.Rd | 5 man/chgColNameCPLEX.Rd | 5 man/chgColTypeCPLEX.Rd | 5 man/chgColsBndsCPLEX.Rd | 5 man/chgMIPstartsCPLEX.Rd | 5 man/chgNameCPLEX.Rd | 5 man/chgObjCPLEX.Rd | 5 man/chgProbNameCPLEX.Rd | 5 man/chgProbTypeCPLEX.Rd | 5 man/chgQPcoefCPLEX.Rd | 5 man/chgRhsCPLEX.Rd | 5 man/chgRngValCPLEX.Rd | 5 man/chgRowNameCPLEX.Rd | 5 man/chgSenseCPLEX.Rd | 5 man/chgTerminateCPLEX.Rd | 5 man/cleanupCoefCPLEX.Rd | 5 man/cloneProbCPLEX.Rd | 5 man/closeEnvCPLEX.Rd | 5 man/closeFileCPLEX.Rd | 5 man/closeProbCPLEX.Rd | 5 man/completelpCPLEX.Rd | 5 man/copyBaseCPLEX.Rd | 5 man/copyColTypeCPLEX.Rd | 5 man/copyLpCPLEX.Rd | 5 man/copyLpwNamesCPLEX.Rd | 5 man/copyObjNameCPLEX.Rd | 5 man/copyOrderCPLEX.Rd | 5 man/copyPartBaseCPLEX.Rd | 5 man/copyQPsepCPLEX.Rd | 5 man/copyQuadCPLEX.Rd | 5 man/copyStartCPLEX.Rd | 5 man/cplexAPI-package.Rd | 5 man/cplexConstants.Rd | 5 man/cplexError-class.Rd | 5 man/cplexPtr-class.Rd | 5 man/delChannelCPLEX.Rd | 5 man/delColsCPLEX.Rd | 5 man/delFpDestCPLEX.Rd | 5 man/delIndConstrsCPLEX.Rd | 5 man/delMIPstartsCPLEX.Rd | 5 man/delNamesCPLEX.Rd | 5 man/delProbCPLEX.Rd | 5 man/delQConstrsCPLEX.Rd | 5 man/delRowsCPLEX.Rd | 5 man/delSetColsCPLEX.Rd | 5 man/delSetRowsCPLEX.Rd | 5 man/delTerminateCPLEX.Rd | 5 man/disconnectChannelCPLEX.Rd | 5 man/dualWriteCPLEX.Rd | 5 man/dualoptCPLEX.Rd | 5 man/feasOptCPLEX.Rd | 5 man/fileputCPLEX.Rd | 5 man/flushChannelCPLEX.Rd | 5 man/flushStdChannelsCPLEX.Rd | 5 man/freePresolveCPLEX.Rd | 5 man/getBaseCPLEX.Rd | 5 man/getBestObjValCPLEX.Rd | 5 man/getChannelsCPLEX.Rd | 5 man/getChgParmCPLEX.Rd | 5 man/getCoefCPLEX.Rd | 5 man/getColIndexCPLEX.Rd | 5 man/getColInfeasCPLEX.Rd | 5 man/getColNameCPLEX.Rd | 5 man/getColTypeCPLEX.Rd | 5 man/getColsCPLEX.Rd | 5 man/getConflictCPLEX.Rd | 5 man/getConflictExtCPLEX.Rd | 5 man/getCutoffCPLEX.Rd | 5 man/getDblParmCPLEX.Rd | 5 man/getDblQualCPLEX.Rd | 5 man/getDbsCntCPLEX.Rd | 5 man/getDjCPLEX.Rd | 5 man/getErrorStrCPLEX.Rd | 5 man/getGradCPLEX.Rd | 5 man/getIndConstrCPLEX.Rd | 5 man/getInfoDblParmCPLEX.Rd | 5 man/getInfoIntParmCPLEX.Rd | 5 man/getInfoLongParmCPLEX.Rd | 5 man/getInfoStrParmCPLEX.Rd | 5 man/getIntParmCPLEX.Rd | 5 man/getIntQualCPLEX.Rd | 5 man/getItCntCPLEX.Rd | 5 man/getLogFileCPLEX.Rd | 5 man/getLongParmCPLEX.Rd | 5 man/getLowBndsIdsCPLEX.Rd | 5 man/getLowerBndsCPLEX.Rd | 5 man/getMIPrelGapCPLEX.Rd | 5 man/getMIPstartIndexCPLEX.Rd | 5 man/getMIPstartNameCPLEX.Rd | 5 man/getMIPstartsCPLEX.Rd | 5 man/getMethodCPLEX.Rd | 5 man/getNumColsCPLEX.Rd | 5 man/getNumMIPstartsCPLEX.Rd | 5 man/getNumNnzCPLEX.Rd | 5 man/getNumQPnzCPLEX.Rd | 5 man/getNumQuadCPLEX.Rd | 5 man/getNumRowsCPLEX.Rd | 5 man/getObjCPLEX.Rd | 5 man/getObjDirCPLEX.Rd | 5 man/getObjNameCPLEX.Rd | 5 man/getObjOffsetCPLEX.Rd | 5 man/getObjValCPLEX.Rd | 5 man/getOrderCPLEX.Rd | 5 man/getParmNameCPLEX.Rd | 5 man/getParmNumCPLEX.Rd | 5 man/getParmTypeCPLEX.Rd | 5 man/getParmValCPLEX.Rd | 5 man/getPhase1CntCPLEX.Rd | 5 man/getPiCPLEX.Rd | 5 man/getPreStatCPLEX.Rd | 5 man/getProbNameCPLEX.Rd | 5 man/getProbTypeCPLEX.Rd | 5 man/getProbVarCPLEX.Rd | 5 man/getQConstrCPLEX.Rd | 5 man/getQPcoefCPLEX.Rd | 5 man/getQuadCPLEX.Rd | 5 man/getRedLpCPLEX.Rd | 5 man/getRhsCPLEX.Rd | 5 man/getRngValCPLEX.Rd | 5 man/getRowIndexCPLEX.Rd | 5 man/getRowInfeasCPLEX.Rd | 5 man/getRowNameCPLEX.Rd | 5 man/getRowsCPLEX.Rd | 5 man/getSenseCPLEX.Rd | 5 man/getSiftItCntCPLEX.Rd | 5 man/getSiftPase1CntCPLEX.Rd | 5 man/getSlackCPLEX.Rd | 5 man/getStatCPLEX.Rd | 5 man/getStatStrCPLEX.Rd | 5 man/getStrParmCPLEX.Rd | 5 man/getSubMethodCPLEX.Rd | 5 man/getSubStatCPLEX.Rd | 5 man/getTimeCPLEX.Rd | 5 man/getUppBndsIdsCPLEX.Rd | 5 man/getUpperBndsCPLEX.Rd | 5 man/getVersionCPLEX.Rd | 5 man/hybbaroptCPLEX.Rd | 5 man/hybnetoptCPLEX.Rd | 5 man/initProbCPLEX.Rd | 5 man/lpoptCPLEX.Rd | 5 man/mipoptCPLEX.Rd | 5 man/newColsCPLEX.Rd | 5 man/newRowsCPLEX.Rd | 5 man/objSaCPLEX.Rd | 5 man/openEnvCPLEX.Rd | 5 man/openFileCPLEX.Rd | 5 man/openProbCPLEX.Rd | 5 man/ordWriteCPLEX.Rd | 5 man/preslvWriteCPLEX.Rd | 5 man/presolveCPLEX.Rd | 5 man/primoptCPLEX.Rd | 5 man/printTerminateCPLEX.Rd | 5 man/qpoptCPLEX.Rd | 5 man/readCopyBaseCPLEX.Rd | 5 man/readCopyMIPstartsCPLEX.Rd | 5 man/readCopyOrderCPLEX.Rd | 5 man/readCopyParmCPLEX.Rd | 5 man/readCopyProbCPLEX.Rd | 5 man/readCopySolCPLEX.Rd | 5 man/refineConflictCPLEX.Rd | 5 man/refineConflictExtCPLEX.Rd | 5 man/refineMIPstartConflictCPLEX.Rd | 5 man/refineMIPstartConflictExtCPLEX.Rd | 5 man/return_codeCPLEX.Rd | 5 man/rhsSaCPLEX.Rd | 5 man/setDblParmCPLEX.Rd | 5 man/setDefaultParmCPLEX.Rd | 5 man/setIntParmCPLEX.Rd | 5 man/setLogFileCPLEX.Rd | 5 man/setLongParmCPLEX.Rd | 5 man/setObjDirCPLEX.Rd | 5 man/setStrParmCPLEX.Rd | 5 man/setTerminateCPLEX.Rd | 5 man/siftoptCPLEX.Rd | 5 man/solWriteCPLEX.Rd | 5 man/solnInfoCPLEX.Rd | 5 man/solutionCPLEX.Rd | 5 man/status_codeCPLEX.Rd | 5 man/tightenBndsCPLEX.Rd | 5 man/tuneParmCPLEX.Rd | 5 man/unscaleProbCPLEX.Rd | 5 man/writeMIPstartsCPLEX.Rd | 5 man/writeParmCPLEX.Rd | 5 man/writeProbCPLEX.Rd | 5 src/Makevars.win | 2 214 files changed, 845 insertions(+), 635 deletions(-)
Title: Statistical Methods for Anthropometric Data
Description: Statistical methodologies especially developed to analyze anthropometric data. These methods are aimed at providing effective solutions to some commons problems related to Ergonomics and Anthropometry. They are based on clustering, the statistical concept of data depth, statistical shape analysis and archetypal analysis.
Author: Guillermo Vinue, Irene Epifanio, Amelia Simo, M. Victoria Ibanez, Juan Domingo, Guillermo Ayala
Maintainer: Guillermo Vinue <Guillermo.Vinue@uv.es>
Diff between Anthropometry versions 1.5 dated 2015-08-27 and 1.6 dated 2015-11-30
DESCRIPTION | 8 +- MD5 | 104 ++++++++++++++------------- NAMESPACE | 2 NEWS | 14 +++ R/anthrCases.R | 51 +++++-------- R/computSizesHipamAnthropom.R |only R/computSizesTrimowa.R |only R/matPercs.R | 2 R/plotPrototypes.R | 8 +- R/plotTrimmOutl.R | 8 +- R/trimmOutl.R | 57 ++++++--------- inst/doc/Anthropometry.R | 55 ++++++-------- inst/doc/Anthropometry.Rnw | 147 +++++++++++++++++++-------------------- inst/doc/Anthropometry.pdf |binary man/Anthropometry-package.Rd | 6 + man/HartiganShapes.Rd | 113 +++-------------------------- man/LloydShapes.Rd | 98 ++------------------------ man/TDDclust.Rd | 12 +-- man/USAFSurvey.Rd | 4 + man/anthrCases.Rd | 37 ++++----- man/archetypesBoundary.Rd | 23 +++--- man/archetypoids.Rd | 89 +++-------------------- man/array3Dlandm.Rd | 2 man/cdfDissWomenPrototypes.Rd | 50 ++++++------- man/checkBranchLocalIMO.Rd | 3 man/checkBranchLocalMO.Rd | 3 man/computSizesHipamAnthropom.Rd |only man/computSizesTrimowa.Rd |only man/descrDissTrunks.Rd | 17 ++-- man/figures8landm.Rd | 6 - man/getDistMatrix.Rd | 6 - man/hipamAnthropom.Rd | 36 +++------ man/matPercs.Rd | 28 +++---- man/nearestToArchetypes.Rd | 21 ++--- man/optraShapes.Rd | 2 man/overlapBiclustersByRows.Rd | 2 man/percentilsArchetypoid.Rd | 23 +++--- man/plotPrototypes.Rd | 98 +++----------------------- man/plotTreeHipamAnthropom.Rd | 22 +---- man/plotTrimmOutl.Rd | 82 +++------------------ man/preprocessing.Rd | 3 man/projShapes.Rd | 31 +++----- man/qtranShapes.Rd | 2 man/screeArchetypal.Rd | 47 ++++++------ man/shapes3dShapes.Rd | 22 ++--- man/skeletonsArchetypal.Rd | 32 -------- man/stepArchetypesRawData.Rd | 24 +++--- man/stepArchetypoids.Rd | 19 ++--- man/trimmOutl.Rd | 34 ++++----- man/trimmedLloydShapes.Rd | 20 ++--- man/trimmedoid.Rd | 8 -- man/trimowa.Rd | 32 ++++++-- man/xyplotPCArchetypes.Rd | 20 +++-- vignettes/AA.pdf |binary vignettes/Anthropometry.Rnw | 147 +++++++++++++++++++-------------------- 55 files changed, 656 insertions(+), 1024 deletions(-)
Title: Survey Planning Tools
Description: Tools for sample survey planning, including sample size calculation, estimation of expected precision for the estimates of totals, and calculation of optimal sample size allocation.
Author: Juris Breidaks [aut, cre],
Martins Liberts [aut],
Janis Jukams [aut]
Maintainer: Juris Breidaks <rcsb@csb.gov.lv>
Diff between surveyplanning versions 0.6 dated 2015-11-25 and 0.8 dated 2015-11-30
DESCRIPTION | 8 +++--- MD5 | 10 +++---- R/dom_optimal_allocation.R | 55 ++++++++++++++++++++++-------------------- R/s2.R | 4 ++- man/dom_optimal_allocation.Rd | 5 --- man/surveyplanning-package.Rd | 4 +-- 6 files changed, 44 insertions(+), 42 deletions(-)
More information about surveyplanning at CRAN
Permanent link
Title: Genome-Wide Association Analysis of a Biomarker Accounting for
Limit of Detection
Description: Genome-wide association (GWAS) analyses
of a biomarker that account for the limit of detection.
Author: Ahmad Vaez, Ilja M. Nolte, Peter J. van der Most
Maintainer: Ilja M. Nolte <i.m.nolte@umcg.nl>
Diff between lodGWAS versions 1.0-6 dated 2015-10-26 and 1.0-7 dated 2015-11-30
lodGWAS-1.0-6/lodGWAS/R/packaging_v10-6.r |only lodGWAS-1.0-6/lodGWAS/inst/doc/lodGWAS_changelog_v1_0_6.txt |only lodGWAS-1.0-7/lodGWAS/DESCRIPTION | 8 ++++---- lodGWAS-1.0-7/lodGWAS/MD5 | 12 ++++++------ lodGWAS-1.0-7/lodGWAS/R/packaging_v10-7.r |only lodGWAS-1.0-7/lodGWAS/inst/doc/lodGWAS_changelog_v1_0_7.txt |only lodGWAS-1.0-7/lodGWAS/man/lodGWAS-package.Rd | 4 ++-- lodGWAS-1.0-7/lodGWAS/man/lod_GWAS.Rd | 12 ++++++------ lodGWAS-1.0-7/lodGWAS/man/lod_QC.Rd | 2 +- 9 files changed, 19 insertions(+), 19 deletions(-)
Title: Help to Fit of a Parametric Distribution to Non-Censored or
Censored Data
Description: Extends the fitdistr function (of the MASS package) with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left censored, right censored and interval censored values, with several lower and upper bounds. In addition to maximum likelihood estimation (MLE), the package provides moment matching (MME), quantile matching (QME) and maximum goodness-of-fit estimation (MGE) methods (available only for non-censored data). Weighted versions of MLE, MME and QME are available.
Author: Marie Laure Delignette-Muller [aut, cre],
Christophe Dutang [aut],
Regis Pouillot [ctb],
Jean-Baptiste Denis [ctb]
Maintainer: Marie Laure Delignette-Muller <marielaure.delignettemuller@vetagro-sup.fr>
Diff between fitdistrplus versions 1.0-5 dated 2015-09-21 and 1.0-6 dated 2015-11-30
DESCRIPTION | 14 +++++++------- MD5 | 11 ++++++----- R/util-startarg.R | 12 ++++++------ inst/NEWS | 7 +++++++ inst/doc/paper2JSS.pdf |binary man/fitdist.Rd | 22 +++++++++++++++++++++- tests/test-startingvalues.R |only 7 files changed, 47 insertions(+), 19 deletions(-)
Title: R Interface to 'EPP-Lab', a Java Program for Exploratory
Projection Pursuit
Description: An R Interface to 'EPP-lab' v1.0. 'EPP-lab' is a Java program for
projection pursuit using genetic algorithms written by Alain Berro and S. Larabi
Marie-Sainte and is included in the package. The 'EPP-lab' sources are available
under https://github.com/fischuu/EPP-lab.git.
Author: Daniel Fischer, Alain Berro, Klaus Nordhausen, Anne Ruiz-Gazen
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>
Diff between REPPlab versions 0.9.2 dated 2015-10-02 and 0.9.3 dated 2015-11-30
DESCRIPTION | 18 ++++++++++------- MD5 | 44 +++++++++++++++++++++---------------------- NAMESPACE | 2 - R/EPPlabAgg.R | 2 - R/REPPlab-package.R | 19 ++++++++++-------- inst/ChangeLog | 7 ++++++ man/EPPlab.Rd | 6 +++-- man/EPPlabAgg.Rd | 28 ++++++++++++++------------- man/EPPlabOutlier.Rd | 8 ++++--- man/REPPlab-package.Rd | 11 ++++++---- man/ReliabilityData.Rd | 14 +++++++------ man/WhitenSVD.Rd | 5 +++- man/coef.epplab.Rd | 4 ++- man/fitted.epplab.Rd | 4 ++- man/pairs.epplab.Rd | 4 ++- man/plot.epplab.Rd | 4 ++- man/plot.epplabOutlier.Rd | 8 ++++--- man/predict.epplab.Rd | 4 ++- man/print.epplab.Rd | 4 ++- man/print.epplabOutlier.Rd | 8 ++++--- man/screeplot.epplab.Rd | 4 ++- man/summary.epplab.Rd | 4 ++- man/summary.epplabOutlier.Rd | 8 ++++--- 23 files changed, 135 insertions(+), 85 deletions(-)
Title: R Dependency Injection
Description: R dependency injection framework. Dependency injection allows
a program design to follow the dependency inversion principle. The user
delegates to external code (the injector) the responsibility of providing its
dependencies. This separates the responsibilities of use and construction.
Author: Lev Kuznetsov
Maintainer: Lev Kuznetsov <levk@jimmy.harvard.edu>
Diff between injectoR versions 0.2.3 dated 2015-11-23 and 0.2.4 dated 2015-11-30
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/injector.R | 12 ++++++------ 3 files changed, 12 insertions(+), 12 deletions(-)
Title: Modern Functions for Qualitative Comparative Analysis
Description: An extensive set of functions to perform Qualitative Comparative Analysis:
crisp sets ('csQCA'), temporal ('tQCA'), multi-value ('mvQCA') and fuzzy sets ('fsQCA'),
using a GUI - graphical user interface.
QCA is a methodology that bridges the qualitative and quantitative divide
in social science research. It uses a boolean algorithm that results in a minimal
causal combination which explains a given phenomenon.
Author: Adrian Dusa [aut, cre, cph],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/gui/www/shared/jquery-AUTHORS.txt),
Vasil Dinkov [ctb, cph] (jquery.smartmenus.js library),
Dmitry Baranovskiy [ctb, cph] (raphael.js library),
Thomas Richter [ctb, cph] (raphael.boolean.js library),
Emmanuel Quentin [ctb, cph] (raphael.inline_text_editing.js library),
Jimmy Breck-McKye [ctb, cph] (raphael-paragraph.js library),
Alrik Thiem [ctb] (package QCA versions from 1.0-0 to 1.1-3)
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between QCAGUI versions 1.9-6 dated 2013-03-19 and 2.0 dated 2015-11-30
QCAGUI-1.9-6/QCAGUI/NEWS |only QCAGUI-1.9-6/QCAGUI/R/Rexcel-specific.R |only QCAGUI-1.9-6/QCAGUI/R/analyze-menu.R |only QCAGUI-1.9-6/QCAGUI/R/commander.R |only QCAGUI-1.9-6/QCAGUI/R/data-menu.R |only QCAGUI-1.9-6/QCAGUI/R/file-menu.R |only QCAGUI-1.9-6/QCAGUI/R/globals.R |only QCAGUI-1.9-6/QCAGUI/R/graphs-menu.R |only QCAGUI-1.9-6/QCAGUI/R/ismdi.R |only QCAGUI-1.9-6/QCAGUI/R/sciviews-specific.R |only QCAGUI-1.9-6/QCAGUI/R/startup.R |only QCAGUI-1.9-6/QCAGUI/R/statistics-summaries-menu.R |only QCAGUI-1.9-6/QCAGUI/R/statistics-tables-menu.R |only QCAGUI-1.9-6/QCAGUI/R/utilities.R |only QCAGUI-1.9-6/QCAGUI/inst/doc |only QCAGUI-1.9-6/QCAGUI/inst/etc |only QCAGUI-1.9-6/QCAGUI/man/CFA.Rd |only QCAGUI-1.9-6/QCAGUI/man/Commander-es.Rd |only QCAGUI-1.9-6/QCAGUI/man/Commander.Rd |only QCAGUI-1.9-6/QCAGUI/man/Compute.Rd |only QCAGUI-1.9-6/QCAGUI/man/Hist.Rd |only QCAGUI-1.9-6/QCAGUI/man/Plugins.Rd |only QCAGUI-1.9-6/QCAGUI/man/QCAGUI-package.Rd |only QCAGUI-1.9-6/QCAGUI/man/Rcmdr-internal.Rd |only QCAGUI-1.9-6/QCAGUI/man/Rcmdr.Utilities.Rd |only QCAGUI-1.9-6/QCAGUI/man/Rcmdr.sciviews-specific.Rd |only QCAGUI-1.9-6/QCAGUI/man/RcmdrPager.Rd |only QCAGUI-1.9-6/QCAGUI/man/RecodeDialog.Rd |only QCAGUI-1.9-6/QCAGUI/man/generalizedLinearModel.Rd |only QCAGUI-1.9-6/QCAGUI/man/hierarchicalCluster.Rd |only QCAGUI-1.9-6/QCAGUI/man/linearModel.Rd |only QCAGUI-1.9-6/QCAGUI/man/mergeRows.Rd |only QCAGUI-1.9-6/QCAGUI/man/numSummary.Rd |only QCAGUI-1.9-6/QCAGUI/man/partial.cor.Rd |only QCAGUI-1.9-6/QCAGUI/man/plotMeans.Rd |only QCAGUI-1.9-6/QCAGUI/man/reliability.Rd |only QCAGUI-1.9-6/QCAGUI/man/totPercents.Rd |only QCAGUI-1.9-6/QCAGUI/src/Makevars.win |only QCAGUI-1.9-6/QCAGUI/src/ismdi.c |only QCAGUI-2.0/QCAGUI/DESCRIPTION | 72 ++++--- QCAGUI-2.0/QCAGUI/MD5 | 201 ++++++++++++++------- QCAGUI-2.0/QCAGUI/NAMESPACE | 140 ++++++++------ QCAGUI-2.0/QCAGUI/R/allExpressions.R |only QCAGUI-2.0/QCAGUI/R/base3rows.R |only QCAGUI-2.0/QCAGUI/R/calibrate.R |only QCAGUI-2.0/QCAGUI/R/createChart.R |only QCAGUI-2.0/QCAGUI/R/createMatrix.R |only QCAGUI-2.0/QCAGUI/R/createString.R |only QCAGUI-2.0/QCAGUI/R/deMorgan.R |only QCAGUI-2.0/QCAGUI/R/demoChart.R |only QCAGUI-2.0/QCAGUI/R/eqmcc.R |only QCAGUI-2.0/QCAGUI/R/eqmccLoop.R |only QCAGUI-2.0/QCAGUI/R/export.R |only QCAGUI-2.0/QCAGUI/R/factorize.R |only QCAGUI-2.0/QCAGUI/R/findSubsets.R |only QCAGUI-2.0/QCAGUI/R/findSupersets.R |only QCAGUI-2.0/QCAGUI/R/findTh.R |only QCAGUI-2.0/QCAGUI/R/fuzzyand.R |only QCAGUI-2.0/QCAGUI/R/fuzzyor.R |only QCAGUI-2.0/QCAGUI/R/getRow.R |only QCAGUI-2.0/QCAGUI/R/getSolution.R |only QCAGUI-2.0/QCAGUI/R/intersection.R |only QCAGUI-2.0/QCAGUI/R/is.print.R |only QCAGUI-2.0/QCAGUI/R/onAttach.R |only QCAGUI-2.0/QCAGUI/R/pof.R |only QCAGUI-2.0/QCAGUI/R/possibleNumeric.R |only QCAGUI-2.0/QCAGUI/R/prettyString.R |only QCAGUI-2.0/QCAGUI/R/prettyTable.R |only QCAGUI-2.0/QCAGUI/R/recode.R |only QCAGUI-2.0/QCAGUI/R/rowDominance.R |only QCAGUI-2.0/QCAGUI/R/runGUI.R |only QCAGUI-2.0/QCAGUI/R/solveChart.R |only QCAGUI-2.0/QCAGUI/R/sortMatrix.R |only QCAGUI-2.0/QCAGUI/R/sortVector.R |only QCAGUI-2.0/QCAGUI/R/string.R |only QCAGUI-2.0/QCAGUI/R/superSubset.R |only QCAGUI-2.0/QCAGUI/R/superSubsetOld.R |only QCAGUI-2.0/QCAGUI/R/truthTable.R |only QCAGUI-2.0/QCAGUI/R/verifyQCA.R |only QCAGUI-2.0/QCAGUI/R/writePrimeimp.R |only QCAGUI-2.0/QCAGUI/R/writeSolution.R |only QCAGUI-2.0/QCAGUI/data |only QCAGUI-2.0/QCAGUI/inst/CITATION | 75 ++++++- QCAGUI-2.0/QCAGUI/inst/ChangeLog |only QCAGUI-2.0/QCAGUI/inst/TODO |only QCAGUI-2.0/QCAGUI/inst/gui |only QCAGUI-2.0/QCAGUI/man/QCAGUI-internal.Rd |only QCAGUI-2.0/QCAGUI/man/QCAGUI.package.Rd |only QCAGUI-2.0/QCAGUI/man/allExpressions.Rd |only QCAGUI-2.0/QCAGUI/man/calibrate.Rd |only QCAGUI-2.0/QCAGUI/man/createMatrix.Rd |only QCAGUI-2.0/QCAGUI/man/d.biodiversity.Rd |only QCAGUI-2.0/QCAGUI/man/d.education.Rd |only QCAGUI-2.0/QCAGUI/man/d.graduate.Rd |only QCAGUI-2.0/QCAGUI/man/d.health.Rd |only QCAGUI-2.0/QCAGUI/man/d.homeless.Rd |only QCAGUI-2.0/QCAGUI/man/d.jobsecurity.Rd |only QCAGUI-2.0/QCAGUI/man/d.napoleon.Rd |only QCAGUI-2.0/QCAGUI/man/d.partybans.Rd |only QCAGUI-2.0/QCAGUI/man/d.represent.Rd |only QCAGUI-2.0/QCAGUI/man/d.socialsecurity.Rd |only QCAGUI-2.0/QCAGUI/man/d.stakeholder.Rd |only QCAGUI-2.0/QCAGUI/man/d.transport.Rd |only QCAGUI-2.0/QCAGUI/man/d.urban.Rd |only QCAGUI-2.0/QCAGUI/man/deMorgan.Rd |only QCAGUI-2.0/QCAGUI/man/demoChart.Rd |only QCAGUI-2.0/QCAGUI/man/eqmcc.Rd |only QCAGUI-2.0/QCAGUI/man/export.Rd |only QCAGUI-2.0/QCAGUI/man/factorize.Rd |only QCAGUI-2.0/QCAGUI/man/findSubsets.Rd |only QCAGUI-2.0/QCAGUI/man/findSupersets.Rd |only QCAGUI-2.0/QCAGUI/man/findTh.Rd |only QCAGUI-2.0/QCAGUI/man/getRow.Rd |only QCAGUI-2.0/QCAGUI/man/intersection.Rd |only QCAGUI-2.0/QCAGUI/man/pof.Rd |only QCAGUI-2.0/QCAGUI/man/recode.Rd |only QCAGUI-2.0/QCAGUI/man/runGUI.Rd |only QCAGUI-2.0/QCAGUI/man/solveChart.Rd |only QCAGUI-2.0/QCAGUI/man/superSubset.Rd |only QCAGUI-2.0/QCAGUI/man/truthTable.Rd |only QCAGUI-2.0/QCAGUI/src/allSol.c |only QCAGUI-2.0/QCAGUI/src/findSubsets.c |only QCAGUI-2.0/QCAGUI/src/m2.c |only QCAGUI-2.0/QCAGUI/src/removeRedundants.c |only QCAGUI-2.0/QCAGUI/src/solveChart.c |only QCAGUI-2.0/QCAGUI/src/superSubset.c |only QCAGUI-2.0/QCAGUI/src/truthTable.c |only 127 files changed, 332 insertions(+), 156 deletions(-)
Title: Discretization-Based Direct Random Sample Generation
Description: Two discretization-based Monte Carlo algorithms, namely the Fu-Wang algorithm and the Wang-Lee algorithm, are provided for random sample generation from a high dimensional distribution of complex structure. The normalizing constant of the target distribution needs not to be known.
Author: Chel Hee Lee [aut, cre],
Liqun Wang [aut]
Maintainer: Chel Hee Lee <gnustats@gmail.com>
Diff between dsample versions 0.91.1.5 dated 2015-07-02 and 0.91.2.2 dated 2015-11-30
dsample-0.91.1.5/dsample/man/summary.dsample.Rd |only dsample-0.91.2.2/dsample/ChangeLog | 8 + dsample-0.91.2.2/dsample/DESCRIPTION | 10 - dsample-0.91.2.2/dsample/MD5 | 16 +- dsample-0.91.2.2/dsample/NAMESPACE | 1 dsample-0.91.2.2/dsample/R/dsample.R | 162 ++++++++++++------------ dsample-0.91.2.2/dsample/demo |only dsample-0.91.2.2/dsample/man/dsample.Rd | 25 +-- dsample-0.91.2.2/dsample/man/plot.Rd |only dsample-0.91.2.2/dsample/man/summary_dsample.Rd |only 10 files changed, 115 insertions(+), 107 deletions(-)