Title: GUI Tools to Process, Analyze and Plot Fisheries Data
Description: The tools you need to process, analyze, combine, integrate and
plot your fishery data: the georeferenced dataset from the Vessel Monitoring
System (VMS), from the Automatic Information System (AIS) or other tracking
devices, as well as the catches or landings dataset from the Logbook or Vessel
Register. Package 'vmsbase' is equipped by Viewer Tools to visually inspect data
at different steps of the analyses and to produce effective outputs for reports
and scientific publications. Viewers are conceived to show the VMS pings, to
visualize single or multiple tracks for fishing vessels, or to represent the VMS
data on Google Viewer, so that the user can produce easy to interpret and more
realistic visualization of both fishing effort and effort behaviour. Package
'vmsbase' represents the implementation of several R routines which have been
developed by the "Tor Vergata" University of Rome Team involved in the Italian
National Program for the Data Collection Framework for Fisheries Data between
2009-2012.
Author: Lorenzo D'Andrea, Tommaso Russo, Antonio Parisi, Stefano Cataudella
Maintainer: Lorenzo D'Andrea <support@vmsbase.org>
Diff between vmsbase versions 2.0 dated 2015-03-10 and 2.1 dated 2015-10-30
DESCRIPTION | 25 ++- MD5 | 120 +++++++++--------- NAMESPACE | 13 +- R/fun_vms_db_clean.R | 141 ++++++++++++--------- R/gui_main.R | 4 R/gui_vms_db_cut.R | 297 ++++++++++++++++++++++++++-------------------- R/gui_vms_db_dep.R | 12 - R/gui_vms_db_intr.R | 82 ++++-------- R/gui_vms_save_bat.R | 38 +++-- R/latsex2dec.R | 14 -- R/lonsex2dec.R | 14 -- R/saveRawVms.R | 40 +++--- README.md | 23 ++- man/Assign_Area.Rd | 2 man/CountMap.Rd | 2 man/Join2shp.Rd | 2 man/bathymetry.Rd | 2 man/gui_dcf_ind.Rd | 2 man/gui_join_lb_vms.Rd | 2 man/gui_lb_db_create.Rd | 4 man/gui_lb_db_edit.Rd | 4 man/gui_lb_db_stat.Rd | 2 man/gui_lb_editraw.Rd | 6 man/gui_lb_met_cla.Rd | 2 man/gui_lb_met_dis.Rd | 4 man/gui_lb_met_edi.Rd | 4 man/gui_main.Rd | 2 man/gui_mark_fis_poi.Rd | 2 man/gui_out_grid.Rd | 4 man/gui_vms_db_are.Rd | 2 man/gui_vms_db_clean.Rd | 11 - man/gui_vms_db_create.Rd | 4 man/gui_vms_db_cut.Rd | 11 - man/gui_vms_db_dep.Rd | 13 -- man/gui_vms_db_intr.Rd | 11 - man/gui_vms_db_sel.Rd | 11 - man/gui_vms_db_stat.Rd | 11 - man/gui_vms_editraw.Rd | 6 man/gui_vms_met_pred.Rd | 11 - man/gui_vms_save_bat.Rd | 11 - man/gui_vms_view_intrp.Rd | 11 - man/gui_vms_view_ping.Rd | 11 - man/gui_vms_view_track.Rd | 11 - man/gui_vms_viz_adv.Rd | 11 - man/gui_vmsdb_mixsou.Rd | 2 man/harbCoo.Rd | 2 man/kno2kmh.Rd | 2 man/latsex2dec.Rd | 2 man/log_Cla.Rd | 2 man/log_DB.Rd | 2 man/log_File.Rd | 2 man/lonsex2dec.Rd | 2 man/plotNet.Rd | 2 man/polymap.Rd | 2 man/que_vms_DB.Rd | 2 man/rad2deg.Rd | 2 man/saveRawLogBook.Rd | 2 man/saveRawVms.Rd | 2 man/vms_DB.Rd | 2 man/vms_File.Rd | 2 man/vmsbase.Rd | 6 61 files changed, 559 insertions(+), 494 deletions(-)
Title: Network Visualization using 'vis.js' Library
Description: Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.
Author: Almende B.V. [aut, cph] (vis.js library in htmlwidgets/lib,
http://visjs.org, http://www.almende.com/home),
Benoit Thieurmel [aut, cre] (R interface)
Maintainer: Benoit Thieurmel <bt@datak.fr>
Diff between visNetwork versions 0.1.1 dated 2015-09-18 and 0.1.2 dated 2015-10-30
DESCRIPTION | 10 MD5 | 97 NAMESPACE | 3 NEWS | 12 R/utils.R | 10 R/visClustering.R | 2 R/visConfigure.R | 3 R/visDocumentation.R | 15 R/visEdges.R | 9 R/visGroups.R | 3 R/visHierarchicalLayout.R | 3 R/visInteraction.R | 3 R/visLayout.R | 5 R/visLegend.R |only R/visNetwork.R | 63 R/visNetworkEvents.R | 3 R/visNodes.R | 8 R/visOptions.R | 77 R/visPhysics.R | 5 README.md | 2 inst/doc/Introduction-to-visNetwork.R | 34 inst/doc/Introduction-to-visNetwork.Rmd | 63 inst/doc/Introduction-to-visNetwork.html | 141 - inst/doc/css/prettify.css | 172 - inst/doc/network/index.html | 3112 +++++++++++++++---------------- inst/doc/network/layout.html | 312 +-- inst/doc/network/manipulation.html | 406 ++-- inst/doc/network/nodes.html | 1429 +++++++------- inst/doc/network/physics.html | 446 ++-- inst/examples |only inst/htmlwidgets/lib/vis/vis.map | 2 inst/htmlwidgets/lib/vis/vis.min.css | 2 inst/htmlwidgets/lib/vis/vis.min.js | 88 inst/htmlwidgets/visNetwork.js | 396 +++ inst/htmlwidgets/visNetwork.yaml | 2 inst/shiny/server.R | 17 man/visClusteringOutliers.Rd | 2 man/visConfigure.Rd | 3 man/visDocumentation.Rd | 4 man/visEdges.Rd | 9 man/visEvents.Rd | 3 man/visGroups.Rd | 3 man/visHierarchicalLayout.Rd | 3 man/visInteraction.Rd | 3 man/visLayout.Rd | 5 man/visLegend.Rd |only man/visNetwork.Rd | 30 man/visNodes.Rd | 8 man/visOptions.Rd | 37 man/visPhysics.Rd | 5 vignettes/Introduction-to-visNetwork.Rmd | 63 51 files changed, 3893 insertions(+), 3240 deletions(-)
Title: Statistical Exploration of Landscapes of Phylogenetic Trees
Description: Tools for the exploration of distributions of phylogenetic trees.
This package includes a shiny interface which can be started from R using
'treescapeServer()'.
Author: Thibaut Jombart [aut],
Michelle Kendall [aut, cre],
Jacob Almagro-Garcia [aut],
Caroline Colijn [aut]
Maintainer: Michelle Kendall <m.kendall@imperial.ac.uk>
Diff between treescape versions 1.0.0 dated 2015-09-11 and 1.8.14 dated 2015-10-30
treescape-1.0.0/treescape/man/penEdgeTree.Rd |only treescape-1.0.0/treescape/man/penEdgeTreematch.Rd |only treescape-1.0.0/treescape/man/rcpp_hello_world.Rd |only treescape-1.0.0/treescape/src/rcpp_hello_world.cpp |only treescape-1.8.14/treescape/DESCRIPTION | 11 treescape-1.8.14/treescape/MD5 | 63 treescape-1.8.14/treescape/NAMESPACE | 5 treescape-1.8.14/treescape/R/RcppExports.R | 18 treescape-1.8.14/treescape/R/findGroves.R | 39 treescape-1.8.14/treescape/R/medTree.R | 98 treescape-1.8.14/treescape/R/metrics.R | 133 - treescape-1.8.14/treescape/R/plotGroves.R | 3 treescape-1.8.14/treescape/R/servers.R | 15 treescape-1.8.14/treescape/R/treescape.R | 68 treescape-1.8.14/treescape/README.md | 92 treescape-1.8.14/treescape/inst/shiny/server.R | 1217 +++++++--- treescape-1.8.14/treescape/inst/shiny/ui.R | 679 +++-- treescape-1.8.14/treescape/inst/shiny/www/bootstrap.simplex.css |only treescape-1.8.14/treescape/inst/shiny/www/html/help.html | 180 + treescape-1.8.14/treescape/inst/shiny/www/styles.css |only treescape-1.8.14/treescape/man/findGroves.Rd | 15 treescape-1.8.14/treescape/man/linearMrca.Rd | 10 treescape-1.8.14/treescape/man/medTree.Rd | 31 treescape-1.8.14/treescape/man/multiDist.Rd | 11 treescape-1.8.14/treescape/man/plotGroves.Rd | 4 treescape-1.8.14/treescape/man/treeDist.Rd | 16 treescape-1.8.14/treescape/man/treeVec.Rd | 12 treescape-1.8.14/treescape/man/treescape.Rd | 24 treescape-1.8.14/treescape/man/treescapeServer.Rd | 4 treescape-1.8.14/treescape/src/RcppExports.cpp | 10 treescape-1.8.14/treescape/tests/testthat/testbasics.R | 27 treescape-1.8.14/treescape/vignettes/figs/findgroves-with-emphasis-1.png |only treescape-1.8.14/treescape/vignettes/figs/treescape3d.png |only treescape-1.8.14/treescape/vignettes/figs/treescapeDensiTree.png |only treescape-1.8.14/treescape/vignettes/figs/treescapeTree.png |only treescape-1.8.14/treescape/vignettes/figs/woodmice-tip-emphasis-1.png |only treescape-1.8.14/treescape/vignettes/treescape.Rmd | 48 treescape-1.8.14/treescape/vignettes/treescape.md | 94 38 files changed, 2031 insertions(+), 896 deletions(-)
Title: Datasets for Agresti and Finlay's "Statistical Methods for the
Social Sciences"
Description: Datasets used in "Statistical Methods for the Social Sciences"
(SMSS) by Alan Agresti and Barbara Finlay.
Author: Jeffrey B. Arnold [aut, cre],
Alan Agresti [cph],
Barbara Finlay [cph]
Maintainer: Jeffrey B. Arnold <jeffrey.arnold@gmail.com>
Diff between smss versions 1.0-1 dated 2013-08-22 and 1.0-2 dated 2015-10-30
DESCRIPTION | 15 +----- MD5 | 80 +++++++++++++++++------------------ NEWS | 7 ++- R/crime2005.R | 4 + build/partial.rdb |binary data/UNdata.rda |binary data/anorexia.rda |binary data/birth.rates.rda |binary data/crime2005.rda |binary data/fertility.gdp.rda |binary data/fl.crime.rda |binary data/house.selling.price.2.rda |binary data/house.selling.price.rda |binary data/inc.ed.race.13p1.rda |binary data/income.credit.rda |binary data/mental.impairment.rda |binary data/oecd.data.rda |binary data/statewide.crime.2.rda |binary data/student.survey.rda |binary data/us.pop.size.rda |binary data/zagat.rda |binary inst/extdata/fl-crime.csv | 10 ++-- inst/scripts/download_agresti_csv.sh | 3 - inst/scripts/save_data.R | 2 man/UNdata.Rd | 12 ++--- man/anorexia.Rd | 12 ++--- man/birth.rates.Rd | 8 +-- man/crime2005.Rd | 10 +++- man/fertility.gdp.Rd | 7 +-- man/fl.crime.Rd | 10 ++-- man/house.selling.price.2.Rd | 10 ++-- man/house.selling.price.Rd | 10 ++-- man/inc.ed.race.13p1.Rd | 10 ++-- man/income.credit.Rd | 15 ++---- man/mental.impairment.Rd | 11 ++-- man/oecd.data.Rd | 13 ++--- man/smss-package.Rd | 21 ++++----- man/statewide.crime.2.Rd | 10 +--- man/student.survey.Rd | 9 +-- man/us.pop.size.Rd | 8 ++- man/zagat.Rd | 9 ++- 41 files changed, 154 insertions(+), 152 deletions(-)
Title: Environments Behaving (Almost) as Lists
Description: List environments are environments that can be indexed similarly to lists, e.g. 'x <- listenv(); x[[2]] <- "b"; names(x)[2] <- "B"; print(x$B)'.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between listenv versions 0.4.0 dated 2015-08-08 and 0.5.0 dated 2015-10-30
listenv-0.4.0/listenv/.Rinstignore |only listenv-0.5.0/listenv/DESCRIPTION | 8 listenv-0.5.0/listenv/MD5 | 26 +-- listenv-0.5.0/listenv/NAMESPACE | 6 listenv-0.5.0/listenv/NEWS | 12 + listenv-0.5.0/listenv/R/get_variable.R | 4 listenv-0.5.0/listenv/R/listenv.R | 225 +++++++++++++++++++++------ listenv-0.5.0/listenv/R/utils.R | 30 --- listenv-0.5.0/listenv/build |only listenv-0.5.0/listenv/inst |only listenv-0.5.0/listenv/man/as.list.listenv.Rd | 8 listenv-0.5.0/listenv/man/listenv.Rd | 18 +- listenv-0.5.0/listenv/man/map.Rd | 42 ++--- listenv-0.5.0/listenv/tests/get_variable.R | 16 + listenv-0.5.0/listenv/tests/listenv.R | 171 ++++++++++++++++++++ listenv-0.5.0/listenv/vignettes |only 16 files changed, 439 insertions(+), 127 deletions(-)
Title: Kernel Estimator and Bandwidth Selection for Density and Its
Derivatives
Description: Smoothing techniques and computing bandwidth selectors of the nth derivative of a probability density for one-dimensional data.
Author: Arsalane Chouaib Guidoum
Maintainer: Arsalane Chouaib Guidoum <acguidoum@usthb.dz>
Diff between kedd versions 1.0.2 dated 2015-01-28 and 1.0.3 dated 2015-10-30
DESCRIPTION | 11 +++++---- MD5 | 53 ++++++++++++++++++++++++------------------------ NAMESPACE | 4 +++ NEWS | 2 + build/vignette.rds |binary inst/doc/Thumbs.db |only inst/doc/intro.Rnw | 2 - inst/doc/intro.pdf |binary inst/doc/kedd.Rnw | 8 +++---- inst/doc/kedd.pdf |binary man/dkde.Rd | 2 - man/h.bcv.Rd | 2 - man/h.ucv.Rd | 2 - man/kedd-package.Rd | 6 ++--- man/kernel.conv.Rd | 2 - man/kernel.fun.Rd | 2 - man/plot.dkde.Rd | 4 +-- man/plot.h.amise.Rd | 2 - man/plot.h.bcv.Rd | 2 - man/plot.h.ccv.Rd | 2 - man/plot.h.mcv.Rd | 2 - man/plot.h.mlcv.Rd | 2 - man/plot.h.tcv.Rd | 2 - man/plot.h.ucv.Rd | 2 - man/plot.kernel.conv.Rd | 2 - man/plot.kernel.fun.Rd | 2 - vignettes/intro.Rnw | 2 - vignettes/kedd.Rnw | 8 +++---- 28 files changed, 68 insertions(+), 60 deletions(-)
Title: Global Value Chains Tools
Description: Several tools for Global Value Chain ('GVC') analysis are
implemented.
Author: Bastiaan Quast [aut, cre],
Victor Kummritz [aut]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between gvc versions 0.5.0 dated 2015-10-05 and 0.5.1 dated 2015-10-30
DESCRIPTION | 10 ++++--- MD5 | 42 ++++++++++++++++---------------- NAMESPACE | 2 - NEWS | 8 ++++++ R/downstream.R | 10 +++---- R/gvc.R | 6 ++++ R/nrca.R | 23 ++++++++++++++++++ R/upstream.R | 10 +++---- README.md | 5 +++ inst/doc/gvc.R | 5 ++- inst/doc/gvc.Rmd | 9 +++---- inst/doc/gvc.html | 69 ++++++++++++++++++++---------------------------------- man/dfddva.Rd | 4 +-- man/dfdfva.Rd | 2 - man/downstream.Rd | 14 +++++----- man/e2r.Rd | 4 +-- man/ffddva.Rd | 2 - man/gvc.Rd | 4 +-- man/i2e.Rd | 4 +-- man/nrca.Rd | 25 ++++++++++++++++++- man/upstream.Rd | 14 +++++----- vignettes/gvc.Rmd | 9 +++---- 22 files changed, 167 insertions(+), 114 deletions(-)
Title: Dynamic Nomograms for Linear, Generalized Linear and
Proportional Hazard Models
Description: Demonstrate the results of an lm(), glm() or coxph() model object as a dynamic nomogram that can be displayed in an 'RStudio' panel or web browser.
Author: Amirhossein Jalali, Alberto Alvarez-Iglesias, Davood Roshan Sangachin, John Newell
Maintainer: Amirhossein Jalali <a.jalali2@nuigalway.ie>
Diff between DynNom versions 1.0.1 dated 2015-03-09 and 2.0 dated 2015-10-30
DynNom-1.0.1/DynNom/man/DynNom-package.Rd |only DynNom-2.0/DynNom/DESCRIPTION | 21 - DynNom-2.0/DynNom/MD5 | 15 - DynNom-2.0/DynNom/NAMESPACE | 9 DynNom-2.0/DynNom/R/DynNom.R | 393 +++++------------------------- DynNom-2.0/DynNom/R/DynNom_coxph.R |only DynNom-2.0/DynNom/R/DynNom_glm.R |only DynNom-2.0/DynNom/R/DynNom_lm.R |only DynNom-2.0/DynNom/man/DynNom.Rd | 65 +++- DynNom-2.0/DynNom/man/DynNom.coxph.Rd |only DynNom-2.0/DynNom/man/DynNom.glm.Rd |only DynNom-2.0/DynNom/man/DynNom.lm.Rd |only 12 files changed, 139 insertions(+), 364 deletions(-)
Title: CShapes Dataset and Utilities
Description: Package for CShapes, a GIS dataset of country boundaries (1946-2015). Includes functions for data extraction and the computation of distance matrices and -lists.
Author: Nils B. Weidmann <nils.weidmann@uni-konstanz.de>, Kristian Skrede Gleditsch <ksg@essex.ac.uk>
Maintainer: Nils B. Weidmann <nils.weidmann@uni-konstanz.de>
Diff between cshapes versions 0.4-2 dated 2013-05-07 and 0.5-1 dated 2015-10-30
cshapes-0.4-2/cshapes/inst/shp/cshapes.qpj |only cshapes-0.4-2/cshapes/inst/shp/cshapes.sbn |only cshapes-0.4-2/cshapes/inst/shp/cshapes.sbx |only cshapes-0.4-2/cshapes/inst/shp/cshapes.shp.xml |only cshapes-0.5-1/cshapes/ChangeLog | 5 + cshapes-0.5-1/cshapes/DESCRIPTION | 17 ++-- cshapes-0.5-1/cshapes/MD5 | 22 ++--- cshapes-0.5-1/cshapes/R/cshp.R | 2 cshapes-0.5-1/cshapes/R/distlist.R | 2 cshapes-0.5-1/cshapes/R/distmatrix.R | 2 cshapes-0.5-1/cshapes/inst/shp/cshapes.dbf |binary cshapes-0.5-1/cshapes/inst/shp/cshapes.shp |binary cshapes-0.5-1/cshapes/inst/shp/cshapes_shapefile_documentation.txt | 37 +++++++--- cshapes-0.5-1/cshapes/man/cshapes-package.Rd | 4 - 14 files changed, 53 insertions(+), 38 deletions(-)
Title: Estimation and Testing of Average Hazard Ratios
Description: Methods for estimation of multivariate average hazard ratios as defined by Kalbfleisch and Prentice. The underlying survival functions of the event of interest in each group can be estimated using either the (weighted) Kaplan-Meier estimator or the Aalen-Johansen estimator for the transition probabilities in Markov multi-state models. Right-censored and left-truncated data is supported. Moreover, the difference in restricted mean survival can be estimated.
Author: Matthias Brueckner <mwb@math.uni-bremen.de>
Maintainer: Matthias Brueckner <mwb@math.uni-bremen.de>
Diff between AHR versions 1.2 dated 2015-07-05 and 1.3 dated 2015-10-30
AHR-1.2/AHR/TODO |only AHR-1.3/AHR/DESCRIPTION | 8 ++++---- AHR-1.3/AHR/MD5 | 11 +++++------ AHR-1.3/AHR/R/AHR-package.R | 2 +- AHR-1.3/AHR/R/ahr.R | 34 ++++++++++++++++++++-------------- AHR-1.3/AHR/R/util.R | 2 +- AHR-1.3/AHR/src/prodlim.cpp | 1 - 7 files changed, 31 insertions(+), 27 deletions(-)