Title: SNP-Set (Sequence) Kernel Association Test
Description: Functions for kernel-regression-based association tests including Burden test, SKAT and SKAT-O. These methods aggregate individual SNP score statistics in a SNP set and efficiently compute SNP-set level p-values.
Author: Seunggeun (Shawn) Lee, with contributions from Larisa Miropolsky and Michael Wu
Maintainer: Seunggeun (Shawn) Lee <leeshawn@umich.edu>
Diff between SKAT versions 1.3.0 dated 2017-05-18 and 1.3.2 dated 2017-07-24
SKAT-1.3.0/SKAT/vignettes/Example1.zip |only SKAT-1.3.2/SKAT/DESCRIPTION | 8 - SKAT-1.3.2/SKAT/MD5 | 54 ++++++------ SKAT-1.3.2/SKAT/R/Binary_Function.R | 6 - SKAT-1.3.2/SKAT/R/Binary_MAIN.R | 28 +++--- SKAT-1.3.2/SKAT/R/Binary_MAIN_ExactBin.R | 12 +- SKAT-1.3.2/SKAT/R/Joint_CommonRare.R | 7 - SKAT-1.3.2/SKAT/R/MAIN.R | 26 +++-- SKAT-1.3.2/SKAT/R/Main_SSD.R | 2 SKAT-1.3.2/SKAT/R/SKAT_EMMAX.R | 54 +++++++----- SKAT-1.3.2/SKAT/R/SSD.R | 28 ++++++ SKAT-1.3.2/SKAT/R/X_Chrom.R | 8 - SKAT-1.3.2/SKAT/inst/doc/SKAT.pdf |binary SKAT-1.3.2/SKAT/man/SKAT.rd | 3 SKAT-1.3.2/SKAT/man/SKATBinary.rd | 3 SKAT-1.3.2/SKAT/man/SKATBinary_Single.rd | 5 - SKAT-1.3.2/SKAT/man/SKAT_ChrX.rd | 3 SKAT-1.3.2/SKAT/man/SKAT_NULL_emmaX.rd | 4 SKAT-1.3.2/SKAT/src/Binary_resampling.cpp | 11 -- SKAT-1.3.2/SKAT/src/bed_reader.cpp | 134 ++++++++++++++++++++++++++++-- SKAT-1.3.2/SKAT/src/bed_reader.h | 24 ++++- SKAT-1.3.2/SKAT/src/error_messages.h | 2 SKAT-1.3.2/SKAT/src/interface_new.cpp | 130 ++++++++++++----------------- SKAT-1.3.2/SKAT/src/interface_to_R.cpp | 33 ++++--- SKAT-1.3.2/SKAT/src/kernel_func.cpp | 2 SKAT-1.3.2/SKAT/src/mwo_reader.cpp | 8 - SKAT-1.3.2/SKAT/src/setid_bim_index.cpp | 4 SKAT-1.3.2/SKAT/src/setid_bim_index.h | 2 SKAT-1.3.2/SKAT/vignettes/Example.zip |only 29 files changed, 384 insertions(+), 217 deletions(-)
Title: Custom Inputs Widgets for Shiny
Description: Some custom inputs widgets to use in Shiny applications, like a toggle switch to replace checkboxes. And other components to pimp your apps.
Author: Victor Perrier [aut, cre],
Fanny Meyer [aut],
Silvio Moreto [ctb, cph] (bootstrap-select),
Ana Carolina [ctb, cph] (bootstrap-select),
caseyjhol [ctb, cph] (bootstrap-select),
Matt Bryson [ctb, cph] (bootstrap-select),
t0xicCode [ctb, cph] (bootstrap-select),
Mattia Larentis [ctb, cph] (Bootstrap Switch),
Emanuele Marchi [ctb, cph] (Bootstrap Switch),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Flatlogic [cph] (Awesome Bootstrap Checkbox),
mouse0270 [ctb, cph] (Material Design Switch),
Tristan Edwards [ctb, cph] (SweetAlert),
Fabian Lindfors [ctb, cph] (multi.js),
Daniel Eden [ctb, cph] (animate.css),
Ganapati V S [ctb, cph] (bttn.css)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between shinyWidgets versions 0.3.0 dated 2017-06-11 and 0.3.2 dated 2017-07-24
DESCRIPTION | 16 + LICENSE | 58 +++++ MD5 | 86 +++++--- NAMESPACE | 6 R/actionBttn.R |only R/attachShinyWidgetsDep.R | 78 ++++++- R/input-awesomecheckbox.R | 2 R/input-awesomeradio.R | 5 R/input-checkboxgroupbuttons.R | 43 ++++ R/input-circlebutton.R | 21 ++ R/input-colorselector.R |only R/input-dropdown.R | 50 ++--- R/input-materialswitch.R | 2 R/input-multi.R | 30 ++- R/input-selectpicker.R | 221 +++++++++++++++++++++- R/input-switch.R | 2 R/progressBars.R | 29 ++ R/shinyWidgetsGallery.R | 6 R/sw-dropdown.R |only R/utils.R | 23 ++ data |only inst/examples/colorSelector |only inst/examples/dropdown |only inst/examples/shinyWidgets/global.R | 24 +- inst/examples/shinyWidgets/server.R | 42 +++- inst/examples/shinyWidgets/ui.R | 140 ++++++++++++++ inst/www/animate |only inst/www/bttn |only inst/www/circleButton/circle-button.css | 48 ++++ inst/www/colorSelector |only inst/www/dropdown |only inst/www/multi/multi-bindings.js |only inst/www/shinyWidgets-bindings.min.js | 2 inst/www/shinyWidgets.css | 287 ++++++++++++++++++++--------- inst/www/shinyWidgets.min.css | 2 inst/www/sw-dropdown |only inst/www/sweetAlert/css/sweetalert.min.css |only inst/www/uglify.R | 26 ++ man/actionBttn.Rd |only man/animateOptions.Rd |only man/animations.Rd |only man/awesomeCheckbox.Rd | 2 man/awesomeRadio.Rd | 4 man/colorSelectorInput.Rd |only man/dropdown.Rd |only man/dropdownButton.Rd | 15 - man/materialSwitch.Rd | 2 man/pickerInput.Rd | 124 +++++++++++- man/tooltipOptions.Rd | 2 man/updateCheckboxGroupButtons.Rd | 42 ++++ man/updatePickerInput.Rd | 83 ++++++++ 51 files changed, 1294 insertions(+), 229 deletions(-)
Title: An API Generator for R
Description: Gives the ability to automatically generate and serve an HTTP API
from R functions using the annotations in the R documentation around your
functions.
Author: Trestle Technology, LLC [aut],
Jeff Allen [cre],
Frans van Dunné [ctb],
SmartBear Software [ctb, cph] (swagger-ui)
Maintainer: Jeff Allen <cran@trestletech.com>
Diff between plumber versions 0.3.2 dated 2017-05-22 and 0.4.2 dated 2017-07-24
plumber-0.3.2/plumber/R/processor-image.R |only plumber-0.3.2/plumber/R/processor.R |only plumber-0.3.2/plumber/man/PlumberProcessor.Rd |only plumber-0.4.2/plumber/DESCRIPTION | 31 plumber-0.4.2/plumber/MD5 | 121 - plumber-0.4.2/plumber/NAMESPACE | 8 plumber-0.4.2/plumber/NEWS.md | 57 plumber-0.4.2/plumber/R/default-handlers.R | 29 plumber-0.4.2/plumber/R/digital-ocean.R | 6 plumber-0.4.2/plumber/R/find-port.R |only plumber-0.4.2/plumber/R/images.R |only plumber-0.4.2/plumber/R/parse-block.R |only plumber-0.4.2/plumber/R/parse-globals.R |only plumber-0.4.2/plumber/R/plumber-static.R |only plumber-0.4.2/plumber/R/plumber-step.R | 60 plumber-0.4.2/plumber/R/plumber.R | 757 ++++++---- plumber-0.4.2/plumber/R/query-string.R | 2 plumber-0.4.2/plumber/R/response.R | 13 plumber-0.4.2/plumber/R/serializer-content-type.R | 9 plumber-0.4.2/plumber/R/serializer-html.R | 6 plumber-0.4.2/plumber/R/serializer-htmlwidget.R | 7 plumber-0.4.2/plumber/R/serializer-json.R | 15 plumber-0.4.2/plumber/R/serializer.R | 12 plumber-0.4.2/plumber/R/session-cookie.R | 9 plumber-0.4.2/plumber/R/shared-secret-filter.R |only plumber-0.4.2/plumber/R/swagger.R |only plumber-0.4.2/plumber/README.md | 34 plumber-0.4.2/plumber/inst/examples/09-content-type/plumber.R | 25 plumber-0.4.2/plumber/inst/examples/11-car-inventory |only plumber-0.4.2/plumber/inst/examples/12-entrypoint |only plumber-0.4.2/plumber/inst/hosted-new.R | 2 plumber-0.4.2/plumber/inst/swagger-ui |only plumber-0.4.2/plumber/man/PlumberEndpoint.Rd |only plumber-0.4.2/plumber/man/addSerializer.Rd | 2 plumber-0.4.2/plumber/man/plumber.Rd | 15 plumber-0.4.2/plumber/man/serializers.Rd |only plumber-0.4.2/plumber/tests/testthat/files/endpoints.R | 1 plumber-0.4.2/plumber/tests/testthat/files/entrypoint |only plumber-0.4.2/plumber/tests/testthat/files/entrypoint-bad |only plumber-0.4.2/plumber/tests/testthat/files/include/test.html | 6 plumber-0.4.2/plumber/tests/testthat/files/plumber.R |only plumber-0.4.2/plumber/tests/testthat/files/serializer.R | 2 plumber-0.4.2/plumber/tests/testthat/files/verbs.R | 5 plumber-0.4.2/plumber/tests/testthat/helper-compare-serializer.R |only plumber-0.4.2/plumber/tests/testthat/helper-mock-request.R |only plumber-0.4.2/plumber/tests/testthat/test-content-type.R | 13 plumber-0.4.2/plumber/tests/testthat/test-cookies.R | 2 plumber-0.4.2/plumber/tests/testthat/test-default-handlers.R |only plumber-0.4.2/plumber/tests/testthat/test-deprecated.R |only plumber-0.4.2/plumber/tests/testthat/test-endpoint.R | 18 plumber-0.4.2/plumber/tests/testthat/test-enumerate.R | 4 plumber-0.4.2/plumber/tests/testthat/test-filters.R | 29 plumber-0.4.2/plumber/tests/testthat/test-find-port.R |only plumber-0.4.2/plumber/tests/testthat/test-globals.R |only plumber-0.4.2/plumber/tests/testthat/test-hookable.R |only plumber-0.4.2/plumber/tests/testthat/test-image.R | 8 plumber-0.4.2/plumber/tests/testthat/test-include.R | 8 plumber-0.4.2/plumber/tests/testthat/test-injection.R | 8 plumber-0.4.2/plumber/tests/testthat/test-parse-block.R |only plumber-0.4.2/plumber/tests/testthat/test-path-subst.R | 9 plumber-0.4.2/plumber/tests/testthat/test-plumber.R | 385 +++++ plumber-0.4.2/plumber/tests/testthat/test-postbody.R | 2 plumber-0.4.2/plumber/tests/testthat/test-preempt.R | 13 plumber-0.4.2/plumber/tests/testthat/test-response.R | 8 plumber-0.4.2/plumber/tests/testthat/test-routing.R | 12 plumber-0.4.2/plumber/tests/testthat/test-serializer-html.R |only plumber-0.4.2/plumber/tests/testthat/test-serializer-htmlwidgets.R | 9 plumber-0.4.2/plumber/tests/testthat/test-serializer-json.R | 8 plumber-0.4.2/plumber/tests/testthat/test-serializer.R | 33 plumber-0.4.2/plumber/tests/testthat/test-sessions.R | 22 plumber-0.4.2/plumber/tests/testthat/test-shared-secret.R |only plumber-0.4.2/plumber/tests/testthat/test-static.R | 75 plumber-0.4.2/plumber/tests/testthat/test-swagger.R |only plumber-0.4.2/plumber/tests/testthat/test-warnings.R | 8 74 files changed, 1285 insertions(+), 623 deletions(-)
Title: Joint Modelling of Repeated Measurements and Time-to-Event Data
Description: Analysis of repeated measurements and time-to-event data via random
effects joint models. Fits the joint models proposed by Henderson and colleagues
<doi:10.1093/biostatistics/1.4.465> (single event time) and by Williamson and
colleagues (2008) <doi:10.1002/sim.3451> (competing risks events time) to a
single continuous repeated measure. The time-to-event data is modelled using a
(cause-specific) Cox proportional hazards regression model with time-varying
covariates. The longitudinal outcome is modelled using a linear mixed effects
model. The association is captured by a latent Gaussian process. The model is
estimated using am Expectation Maximization algorithm. Some plotting functions
and the variogram are also included. This project is funded by the Medical
Research Council (Grant numbers G0400615 and MR/M013227/1).
Author: Pete Philipson [aut],
Ines Sousa [aut],
Peter J. Diggle [aut],
Paula Williamson [aut],
Ruwanthi Kolamunnage-Dona [aut],
Robin Henderson [aut],
Graeme L. Hickey [aut, cre],
Maria Sudell [ctb]
Maintainer: Graeme L. Hickey <graeme.hickey@liverpool.ac.uk>
Diff between joineR versions 1.2.0 dated 2017-05-19 and 1.2.1 dated 2017-07-24
joineR-1.2.0/joineR/vignettes/competing-risks_cache/html/jointmodel_493bf187ababa0c02a316d98330986c8.RData |only joineR-1.2.0/joineR/vignettes/competing-risks_cache/html/jointmodel_493bf187ababa0c02a316d98330986c8.rdb |only joineR-1.2.0/joineR/vignettes/competing-risks_cache/html/jointmodel_493bf187ababa0c02a316d98330986c8.rdx |only joineR-1.2.1/joineR/DESCRIPTION | 8 joineR-1.2.1/joineR/MD5 | 55 +- joineR-1.2.1/joineR/NEWS.md | 18 joineR-1.2.1/joineR/R/aids.R |only joineR-1.2.1/joineR/R/epileptic.R | 4 joineR-1.2.1/joineR/R/heart.valve.R | 3 joineR-1.2.1/joineR/R/joint.object.R |only joineR-1.2.1/joineR/R/liver.R | 26 - joineR-1.2.1/joineR/README.md | 4 joineR-1.2.1/joineR/data/aids.rda |only joineR-1.2.1/joineR/data/liver.rda |binary joineR-1.2.1/joineR/inst/doc/competing-risks.R | 18 joineR-1.2.1/joineR/inst/doc/competing-risks.Rmd | 208 ++++------ joineR-1.2.1/joineR/inst/doc/competing-risks.html | 34 - joineR-1.2.1/joineR/inst/doc/joineR.R | 72 --- joineR-1.2.1/joineR/inst/doc/joineR.html | 4 joineR-1.2.1/joineR/man/aids.Rd |only joineR-1.2.1/joineR/man/epileptic.Rd | 4 joineR-1.2.1/joineR/man/heart.valve.Rd | 3 joineR-1.2.1/joineR/man/joint.object.Rd |only joineR-1.2.1/joineR/man/liver.Rd | 24 - joineR-1.2.1/joineR/vignettes/competing-risks.Rmd | 208 ++++------ joineR-1.2.1/joineR/vignettes/competing-risks_cache/html/__packages | 1 joineR-1.2.1/joineR/vignettes/competing-risks_cache/html/jointmodel_3b687d33bb5a66f8fbf911ef4054f617.RData |only joineR-1.2.1/joineR/vignettes/competing-risks_cache/html/jointmodel_3b687d33bb5a66f8fbf911ef4054f617.rdb |only joineR-1.2.1/joineR/vignettes/competing-risks_cache/html/jointmodel_3b687d33bb5a66f8fbf911ef4054f617.rdx |only joineR-1.2.1/joineR/vignettes/competing-risks_cache/html/jointmodel_ses_d85991199f973f64d3a6957e88aa85b5.RData |binary joineR-1.2.1/joineR/vignettes/joineR_cache/html/heart.valve_jd_257aebb51a26b625ea384c22d20e8121.RData |binary joineR-1.2.1/joineR/vignettes/joineR_cache/html/liver_jm_ab3deed578c671625bfee5424f8a444c.RData |binary joineR-1.2.1/joineR/vignettes/joineR_cache/html/mental_jm_boot_8a0878e546549bb07b4c9d0973a7805d.rdb |binary joineR-1.2.1/joineR/vignettes/joineR_cache/html/mental_jm_boot_8a0878e546549bb07b4c9d0973a7805d.rdx |binary 34 files changed, 306 insertions(+), 388 deletions(-)
Title: High Throughput Sequencing of Stable Isotope Probing Data
Analysis
Description: Functions for analyzing high throughput sequencing
stable isotope probing (HTS-SIP) data.
Analyses include high resolution stable isotope probing (HR-SIP),
multi-window high resolution stable isotope probing (MW-HR-SIP),
and quantitative stable isotope probing (q-SIP).
Author: Nicholas Youngblut [aut, cre],
Samuel Barnett [ctb]
Maintainer: Nicholas Youngblut <nyoungb2@gmail.com>
Diff between HTSSIP versions 1.1.1 dated 2017-05-23 and 1.2.0 dated 2017-07-24
DESCRIPTION | 14 +-- MD5 | 66 +++++++------- NEWS.md | 6 + R/BD_ordinations.R | 2 R/BD_shift.R | 143 +++++++++++++++++++++++++------ R/DESeq2_l2fc.R | 2 R/HTSSIP_sim.R | 11 ++ R/Util.R | 5 + R/delta_BD.R | 2 R/qSIP_atom_excess.R | 20 +++- README.md | 13 +- data/physeq_rep3.rda |binary data/physeq_rep3_qPCR.rda |binary inst/doc/BD_shifts.R | 8 - inst/doc/BD_shifts.Rmd | 10 +- inst/doc/BD_shifts.html | 72 +++++++++------ inst/doc/HTSSIP_intro.html | 6 - inst/doc/HTSSIP_sim.html | 6 - inst/doc/MW_HR_SIP.html | 6 - inst/doc/beta_diversity_ordinations.R | 3 inst/doc/beta_diversity_ordinations.Rmd | 3 inst/doc/beta_diversity_ordinations.html | 15 +-- inst/doc/qSIP.html | 6 - inst/doc/quant_incorp.R | 6 - inst/doc/quant_incorp.Rmd | 6 - inst/doc/quant_incorp.html | 14 +-- man/BD_shift.Rd | 23 +++- man/HTSSIP_sim.Rd | 4 man/SIP_betaDiv_ord.Rd | 2 man/qSIP_atom_excess.Rd | 2 tests/testthat/test-BD_shift.R | 6 - vignettes/BD_shifts.Rmd | 10 +- vignettes/beta_diversity_ordinations.Rmd | 3 vignettes/quant_incorp.Rmd | 6 - 34 files changed, 336 insertions(+), 165 deletions(-)
Title: Hierarchical Item Response Theory Models
Description: Implementation of a class of hierarchical item response
theory (IRT) models where both the mean and the variance of latent preferences
(ability parameters) can depend on observed covariates. The current
implementation includes both the two-parameter latent trait model and the
graded response model. Both are fitted via the Expectation-Maximization (EM)
algorithm. Asymptotic standard errors are derived from the observed information
matrix.
Author: Xiang Zhou [aut, cre]
Maintainer: Xiang Zhou <xiang_zhou@fas.harvard.edu>
Diff between hIRT versions 0.1.0 dated 2017-07-23 and 0.1.1 dated 2017-07-24
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- R/data.R | 2 +- R/hgrm.R | 21 ++++++++++++--------- R/hltm.R | 10 ++++++---- R/sysdata.rda |binary man/hgrm.Rd | 19 ++++++++++++------- man/hltm.Rd | 19 ++++++++++++------- man/nes_econ2008.Rd | 2 +- 9 files changed, 58 insertions(+), 43 deletions(-)
Title: Convert Data from and to 'GeoJSON' or 'TopoJSON'
Description: Convert data to 'GeoJSON' or 'TopoJSON' from various R classes,
including vectors, lists, data frames, shape files, and spatial classes.
geojsonio does not aim to replace packages like 'sp', 'rgdal', 'rgeos',
but rather aims to be a high level client to simplify conversions of data
from and to 'GeoJSON' and 'TopoJSON'.
Author: Scott Chamberlain [aut, cre],
Andy Teucher [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between geojsonio versions 0.3.2 dated 2017-02-06 and 0.3.8 dated 2017-07-24
DESCRIPTION | 8 +-- MD5 | 92 ++++++++++++++++++------------------ NEWS.md | 27 +++++++++- R/as.json.R | 8 +-- R/as_spatial_methods.R | 4 - R/geojson_json.R | 8 +-- R/geojson_list.R | 4 - R/geojson_style.R | 2 R/geojson_write.r | 10 ++- R/mapgist.R | 8 +-- R/zzz.r | 12 +++- README.md | 11 +--- build/vignette.rds |binary inst/doc/geojsonio_vignette.Rmd | 22 +++----- inst/doc/geojsonio_vignette.html | 22 +++----- inst/img/unnamed-chunk-20-1.png |binary inst/vign/geojsonio_vignette.md | 22 +++----- man/as.json.Rd | 1 man/as.location.Rd | 1 man/bounds.Rd | 1 man/canada_cities.Rd | 1 man/centroid.Rd | 1 man/file_to_geojson.Rd | 2 man/geojson-add.Rd | 3 - man/geojson_json.Rd | 9 +-- man/geojson_list.Rd | 5 - man/geojson_read.Rd | 2 man/geojson_sp.Rd | 1 man/geojson_style.Rd | 3 - man/geojson_write.Rd | 7 +- man/geojsonio-deprecated.Rd | 1 man/geojsonio.Rd | 2 man/lint.Rd | 1 man/map_gist.Rd | 9 +-- man/map_leaf.Rd | 1 man/pipe.Rd | 1 man/pretty.Rd | 1 man/projections.Rd | 4 + man/states.Rd | 1 man/topojson_read.Rd | 1 man/us_cities.Rd | 1 man/validate.Rd | 1 tests/testthat/test-as.json.R | 4 - tests/testthat/test-crs_convert.R | 32 ++++++------ tests/testthat/test-geojson_write.R | 91 +++++++++++++++++++++++++++++++++-- tests/testthat/test-sf_classes.R | 7 ++ vignettes/geojsonio_vignette.Rmd | 22 +++----- 47 files changed, 286 insertions(+), 191 deletions(-)
Title: Reproduce Statistical Analyses and Meta-Analyses
Description: Includes data analysis functions (e.g., to calculate effect sizes and 95% Confidence Intervals (CI) on Standardised Effect Sizes (d) for ABBA cross-over repeated-measures experimental designs), data presentation functions (e.g., density curve overlaid on histogram), and the data sets analyzed in different research papers in software engineering (e.g., related to software defect prediction or multi-site experiment concerning the extent to which structured abstracts were clearer and more complete than conventional abstracts) to streamline reproducible research in software engineering.
Author: Lech Madeyski [cre, aut, ctb],
Marian Jureczko [ctb] (Data contributor),
Barbara Kitchenham [ctb] (Data and code contributor),
David Budgen [ctb] (Data contributor),
Pearl Brereton [ctb] (Data contributor),
Jacky Keung [ctb] (Data contributor),
Stuart Charters [ctb] (Data contributor),
Shirley Gibbs [ctb] (Data contributor),
Amnart Pohthong [ctb] (Data contributor)
Maintainer: Lech Madeyski <lech.madeyski@gmail.com>
Diff between reproducer versions 0.1.8 dated 2017-02-12 and 0.1.9 dated 2017-07-24
DESCRIPTION | 11 MD5 | 84 +-- NEWS.md | 10 R/MadeyskiKitchenhamMetaAnalysis.R | 229 +++++++--- data/MadeyskiKitchenham.EUBASdata.rda |binary man/Ciolkowski09ESEM.MetaAnalysis.PBRvsCBRorAR.Rd | 1 man/KitchenhamMadeyski.SimulatedCrossoverDataSets.Rd | 1 man/KitchenhamMadeyskiBudgen16.COCOMO.Rd | 1 man/KitchenhamMadeyskiBudgen16.DiffInDiffData.Rd | 1 man/KitchenhamMadeyskiBudgen16.FINNISH.Rd | 1 man/KitchenhamMadeyskiBudgen16.PolishData.Rd | 1 man/KitchenhamMadeyskiBudgen16.PolishSubjects.Rd | 1 man/KitchenhamMadeyskiBudgen16.SubjectData.Rd | 1 man/Madeyski15EISEJ.OpenProjects.Rd | 1 man/Madeyski15EISEJ.PropProjects.Rd | 1 man/Madeyski15EISEJ.StudProjects.Rd | 1 man/Madeyski15SQJ.NDC.Rd | 1 man/MadeyskiKitchenham.EUBASdata.Rd | 1 man/MadeyskiKitchenham.MetaAnalysis.PBRvsCBRorAR.Rd | 1 man/boxplotAndDensityCurveOnHistogram.Rd | 1 man/boxplotHV.Rd | 1 man/densityCurveOnHistogram.Rd | 1 man/effectSizeCI.Rd | 29 - man/fmt.Rd | 1 man/getEffectSizesABBA.Rd | 4 man/getEffectSizesABBAIgnoringPeriodEffect.Rd | 1 man/getSimulationData.Rd | 1 man/getTheoreticalEffectSizeVariancesABBA.Rd | 1 man/percentageInaccuracyOfLargeSampleVarianceApproximation.Rd | 1 man/plotOutcomesForIndividualsInEachSequenceGroup.Rd | 1 man/printXTable.Rd | 1 man/proportionOfSignificantTValuesUsingCorrectAnalysis.Rd | 1 man/proportionOfSignificantTValuesUsingIncorrectAnalysis.Rd | 1 man/readExcelSheet.Rd | 1 man/reproduceForestPlotRandomEffects.Rd | 1 man/reproduceMixedEffectsAnalysisWithEstimatedVarianceAndExperimentalDesignModerator.Rd | 1 man/reproduceMixedEffectsAnalysisWithExperimentalDesignModerator.Rd | 1 man/reproduceMixedEffectsForestPlotWithExperimentalDesignModerator.Rd | 1 man/reproduceSimulationResultsBasedOn500Reps1000Obs.Rd | 1 man/reproduceTableWithEffectSizesBasedOnMeanDifferences.Rd | 1 man/reproduceTableWithPossibleModeratingFactors.Rd | 1 man/reproduceTableWithSourceDataByCiolkowski.Rd | 1 tests |only 43 files changed, 253 insertions(+), 149 deletions(-)
Title: Projection Based Clustering
Description: A clustering approach for every projection method based on the generalized U*-matrix visualization of a topographic map is made available here. The number of clusters and the cluster structure can be estimated by counting the valleys in a topographic map. If the number of clusters and the clustering method are chosen correctly, then the clusters will be well separated by mountains in the visualization. Most projection methods are wrappers for already available methods in R. However, the neighbor retrieval visualizer (NeRV) is based on C++ source code of the 'dredviz' software package and the Curvilinear Component Analysis (CCA) is translated from 'MATLAB' ('SOM Toolbox' 2.0) to R.
Author: Michael Thrun [aut, cre],
Florian Lerch [aut],
Felix Pape [aut],
Kristian Nybo [cph],
Jarkko Venna [cph]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between ProjectionBasedClustering versions 1.0.0 dated 2017-07-23 and 1.0.1 dated 2017-07-24
ProjectionBasedClustering-1.0.0/ProjectionBasedClustering/man/Cmeasure.Rd |only ProjectionBasedClustering-1.0.1/ProjectionBasedClustering/DESCRIPTION | 14 +++++----- ProjectionBasedClustering-1.0.1/ProjectionBasedClustering/MD5 | 13 ++++----- ProjectionBasedClustering-1.0.1/ProjectionBasedClustering/man/Delaunay4Points.Rd | 7 ++--- ProjectionBasedClustering-1.0.1/ProjectionBasedClustering/man/ICA.Rd | 6 ++-- ProjectionBasedClustering-1.0.1/ProjectionBasedClustering/man/MDS.Rd | 2 - ProjectionBasedClustering-1.0.1/ProjectionBasedClustering/man/NeRV.rd | 5 ++- ProjectionBasedClustering-1.0.1/ProjectionBasedClustering/man/ProjectionBasedClustering-package.Rd | 9 ++++++ 8 files changed, 32 insertions(+), 24 deletions(-)
More information about ProjectionBasedClustering at CRAN
Permanent link
Title: Deconvolute Mixed Genomes with Unknown Proportions
Description: Traditional phasing programs are limited to diploid organisms.
Our method modifies Li and Stephens algorithm with Markov chain Monte Carlo
(MCMC) approaches, and builds a generic framework that allows haplotype searches
in a multiple infection setting. This package is primarily developed as part of
the Pf3k project, which is a global collaboration using the latest
sequencing technologies to provide a high-resolution view of natural variation
in the malaria parasite Plasmodium falciparum. Parasite DNA are extracted from
patient blood sample, which often contains more than one parasite strain, with
unknown proportions. This package is used for deconvoluting mixed haplotypes,
and reporting the mixture proportions from each sample.
Author: Joe Zhu [aut, cre, cph]
Maintainer: Joe Zhu <joe.zhu@well.ox.ac.uk>
Diff between DEploid versions 0.3.2 dated 2016-11-25 and 0.4.1 dated 2017-07-24
DESCRIPTION | 12 MD5 | 119 ++- NAMESPACE | 7 R/DEploidR.R | 114 +++ R/RcppExports.R | 10 R/dEploid.R | 23 README.md | 22 build/vignette.rds |binary inst/CITATION |only inst/doc/dEploid-Arguments.Rmd | 30 + inst/doc/dEploid-Arguments.html | 39 + inst/extdata/deploid.png |only man/DEploid-package.Rd |only man/computeObsWSAF.Rd | 1 man/dEploid.Rd | 4 man/extractCoverageFromTxt.Rd | 1 man/extractCoverageFromVcf.Rd | 1 man/extractPLAF.Rd | 1 man/haplotypePainter.Rd | 8 man/histWSAF.Rd | 10 man/plotAltVsRef.Rd | 12 man/plotObsExpWSAF.Rd | 12 man/plotProportions.Rd | 12 man/plotWSAFvsPLAF.Rd | 12 src/DEploid/dEploid.cpp | 48 - src/DEploid/dEploidIO.cpp | 323 +++++++++- src/DEploid/dEploidIO.hpp | 158 ++++- src/DEploid/debug/mcmcDebug.cpp | 4 src/DEploid/debug/vcfReaderDebug.cpp | 4 src/DEploid/exceptions.hpp | 48 + src/DEploid/export/dEploidIOExport.cpp | 249 +++----- src/DEploid/export/dEploidIOExportPosteriorProb.cpp | 129 ++-- src/DEploid/export/writeMcmcRelated.cpp |only src/DEploid/ibd.cpp |only src/DEploid/ibd.hpp |only src/DEploid/mcmc.cpp | 600 +++++++++++++++++--- src/DEploid/mcmc.hpp | 75 ++ src/DEploid/panel.cpp | 76 ++ src/DEploid/panel.hpp | 33 - src/DEploid/random/fastfunc.cpp | 4 src/DEploid/random/fastfunc.hpp | 4 src/DEploid/random/mersenne_twister.cpp | 4 src/DEploid/random/mersenne_twister.hpp | 4 src/DEploid/random/random_generator.cpp | 4 src/DEploid/random/random_generator.hpp | 4 src/DEploid/txtReader.cpp | 17 src/DEploid/txtReader.hpp | 10 src/DEploid/updateHap.cpp | 163 ++++- src/DEploid/updateHap.hpp | 61 +- src/DEploid/utility.cpp | 86 ++ src/DEploid/utility.hpp | 46 + src/DEploid/variantIndex.cpp | 8 src/DEploid/variantIndex.hpp | 8 src/DEploid/vcfReader.cpp | 4 src/DEploid/vcfReader.hpp | 4 src/Makevars | 8 src/Makevars.win | 8 src/RcppExports.cpp | 8 src/dEploidr.cpp | 53 - src/init.c |only src/registerDynamicSymbol.c |only tests/testthat/pf3k-dEploid.hap |only tests/testthat/pf3k-dEploid.llk |only tests/testthat/pf3k-dEploid.prop |only tests/testthat/test-DEploid_tools.R | 35 - vignettes/dEploid-Arguments.Rmd | 30 + 66 files changed, 2120 insertions(+), 650 deletions(-)
Title: Modelling Functions that Work with the Pipe
Description: Functions for modelling that help you seamlessly integrate
modelling into a pipeline of data manipulation and visualisation.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between modelr versions 0.1.0 dated 2016-08-31 and 0.1.1 dated 2017-07-24
DESCRIPTION | 10 +- MD5 | 65 +++++++------ NAMESPACE | 8 + NEWS.md |only R/bootstrap.R | 5 - R/cross-validation.R | 2 R/formulas.R | 29 ++++- R/na-warn.R | 2 R/permute.R |only R/quality.R | 2 R/typical.R | 2 README.md | 189 +++++++++++++++++++++++++++++++++++++-- man/add_predictions.Rd | 3 man/add_predictors.Rd | 1 man/add_residuals.Rd | 3 man/bootstrap.Rd | 3 man/crossv_mc.Rd | 3 man/data_grid.Rd | 1 man/fit_with.Rd | 1 man/formulas.Rd | 3 man/geom_ref_line.Rd | 1 man/heights.Rd | 1 man/model-quality.Rd | 7 - man/model_matrix.Rd | 1 man/na.warn.Rd | 3 man/permute.Rd |only man/pipe.Rd | 1 man/resample.Rd | 1 man/resample_bootstrap.Rd | 1 man/resample_partition.Rd | 1 man/resample_permutation.Rd |only man/seq_range.Rd | 1 man/sim.Rd | 1 man/typical.Rd | 3 tests/testthat/test-formulas.R | 6 + tests/testthat/test-resampling.R |only 36 files changed, 275 insertions(+), 85 deletions(-)
Title: Joyplots in 'ggplot2'
Description: Joyplots provide a convenient way of visualizing changes in distributions over
time or space. This package enables the creation of such plots in 'ggplot2'.
Author: Claus O. Wilke [cre, aut],
RStudio [cph]
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between ggjoy versions 0.1 dated 2017-07-14 and 0.2.0 dated 2017-07-24
DESCRIPTION | 12 +- MD5 | 43 +++++---- NAMESPACE | 7 + NEWS |only R/data.R | 44 ++++++++- R/geoms-gradient.R |only R/geoms.R | 33 +++---- R/stats.R | 190 ++++++++++++++++++++++++++++++++++++++--- README.md | 65 ++++++++------ build/vignette.rds |binary data/Catalan_elections.rda |only data/lincoln_weather.rda |binary inst/doc/gallery.R |only inst/doc/gallery.Rmd |only inst/doc/gallery.html |only inst/doc/introduction.R | 41 +++++--- inst/doc/introduction.Rmd | 74 ++++++++++----- inst/doc/introduction.html | 90 ++++++++++++------- man/Catalan_elections.Rd |only man/figures |only man/geom_joy.Rd | 20 +--- man/geom_ridgeline.Rd | 1 man/geom_ridgeline_gradient.Rd |only man/lincoln_weather.Rd | 31 +++++- man/stat_binline.Rd |only man/stat_joy.Rd | 5 - vignettes/gallery.Rmd |only vignettes/introduction.Rmd | 74 ++++++++++----- 28 files changed, 533 insertions(+), 197 deletions(-)
Title: EMF Graphics Output Device
Description: Output graphics to EMF+/EMF.
Author: Philip Johnson
Maintainer: Philip Johnson <plfj@umd.edu>
Diff between devEMF versions 3.5 dated 2017-06-10 and 3.6 dated 2017-07-24
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 10 +++++++++- inst/afm/README | 2 +- src/devEMF.cpp | 34 ++++++++++++++++++++-------------- src/emf.h | 39 +++++++++++++++++++++------------------ 6 files changed, 60 insertions(+), 43 deletions(-)
Title: Simulate Models Based on the Generalized Linear Model
Description: Easily simulates regression models,
including both simple regression and generalized linear mixed
models with up to three level of nesting. Power simulations that are
flexible allowing the specification of missing data, unbalanced designs,
and different random error distributions are built into the package.
Author: Brandon LeBeau [aut, cre]
Maintainer: Brandon LeBeau <lebebr01+simglm@gmail.com>
Diff between simglm versions 0.5.0 dated 2017-05-25 and 0.6.0 dated 2017-07-24
DESCRIPTION | 6 MD5 | 88 +++--- NEWS.md | 19 + R/data_glm.r | 89 ++++--- R/pow_sim_glm.r | 44 ++- R/sim_glm_func.r | 119 ++++++--- R/sim_pow.r | 6 R/sim_reg.r | 36 ++ R/sim_reg_func.r | 7 R/simglm.r |only README.md | 21 + build/vignette.rds |binary inst/doc/GeneralizedModels.R | 27 +- inst/doc/GeneralizedModels.Rmd | 30 +- inst/doc/GeneralizedModels.html | 363 +++++----------------------- inst/doc/Intro.R | 6 inst/doc/Intro.Rmd | 6 inst/doc/Intro.html | 482 +++++++++++++++++++------------------- inst/doc/Missing.html | 340 +++++++++++++------------- inst/doc/Power.R | 2 inst/doc/Power.Rmd | 2 inst/doc/Power.html | 236 +++++++++--------- inst/doc/unbalanced.html | 4 inst/shiny_examples/demo/global.r | 20 + inst/shiny_examples/demo/server.r | 203 ++++++++++------ inst/shiny_examples/demo/ui.r | 128 +++++----- man/data_glm_nested.Rd | 11 man/data_glm_nested3.Rd | 12 man/data_glm_single.Rd | 11 man/sim_glm.Rd | 31 +- man/sim_glm_nested.Rd | 10 man/sim_glm_nested3.Rd | 12 man/sim_glm_single.Rd | 11 man/sim_pow_glm.Rd | 15 - man/sim_pow_glm_nested.Rd | 10 man/sim_pow_glm_nested3.Rd | 10 man/sim_pow_glm_single.Rd | 6 man/simglm.Rd |only tests/testthat/test_data_glm.r | 10 tests/testthat/test_dimensions.r | 8 tests/testthat/test_model_spec.r | 9 tests/testthat/test_power_struc.r | 15 + tests/testthat/test_power_vary.r | 4 vignettes/GeneralizedModels.Rmd | 30 +- vignettes/Intro.Rmd | 6 vignettes/Power.Rmd | 2 46 files changed, 1342 insertions(+), 1165 deletions(-)
Title: Complement to 'Modern Data Science with R'
Description: A complement to *Modern Data
Science with R* (ISBN: 978-1498724487, publisher URL:
<https://www.crcpress.com/Modern-Data-Science-with-R/Baumer-Kaplan-Horton/p/book/9781498724487>).
This package contains all of the data and code necessary to
complete exercises and reproduce examples from the text. It also
facilitates connections to the SQL database server used in the book.
Author: Ben Baumer [aut, cre],
Nicholas Horton [aut],
Daniel Kaplan [aut]
Maintainer: Ben Baumer <ben.baumer@gmail.com>
Diff between mdsr versions 0.1.3 dated 2016-08-29 and 0.1.4 dated 2017-07-24
mdsr-0.1.3/mdsr/man/Cancer.Rd |only mdsr-0.1.4/mdsr/DESCRIPTION | 15 ++++--- mdsr-0.1.4/mdsr/MD5 | 58 +++++++++++++++-------------- mdsr-0.1.4/mdsr/NAMESPACE | 6 ++- mdsr-0.1.4/mdsr/NEWS.md | 6 +++ mdsr-0.1.4/mdsr/R/NCI60.R |only mdsr-0.1.4/mdsr/R/attach.R |only mdsr-0.1.4/mdsr/R/data.R | 38 ++++++++++++++++--- mdsr-0.1.4/mdsr/R/scidb.R | 13 +++--- mdsr-0.1.4/mdsr/R/themes.R | 2 - mdsr-0.1.4/mdsr/README.md | 6 +-- mdsr-0.1.4/mdsr/data/NCI60_tiny.rda |only mdsr-0.1.4/mdsr/data/datalist | 1 mdsr-0.1.4/mdsr/man/CIACountries.Rd | 3 - mdsr-0.1.4/mdsr/man/Cherry.Rd | 1 mdsr-0.1.4/mdsr/man/CholeraDeaths.Rd | 1 mdsr-0.1.4/mdsr/man/DataSciencePapers.Rd | 1 mdsr-0.1.4/mdsr/man/Elections.Rd | 1 mdsr-0.1.4/mdsr/man/MLB_teams.Rd | 1 mdsr-0.1.4/mdsr/man/Macbeth_raw.Rd | 1 mdsr-0.1.4/mdsr/man/MedicareCharges.Rd | 1 mdsr-0.1.4/mdsr/man/MedicareProviders.Rd | 1 mdsr-0.1.4/mdsr/man/Minneapolis2013.Rd | 1 mdsr-0.1.4/mdsr/man/NCI60_tiny.Rd |only mdsr-0.1.4/mdsr/man/OrdwayBirds.Rd | 1 mdsr-0.1.4/mdsr/man/SAT_2010.Rd | 1 mdsr-0.1.4/mdsr/man/Violations.Rd | 5 +- mdsr-0.1.4/mdsr/man/Votes.Rd | 3 - mdsr-0.1.4/mdsr/man/WorldCities.Rd | 1 mdsr-0.1.4/mdsr/man/etl_NCI60.Rd |only mdsr-0.1.4/mdsr/man/make_babynames_dist.Rd | 1 mdsr-0.1.4/mdsr/man/src_scidb.Rd | 9 ++-- mdsr-0.1.4/mdsr/man/theme_mdsr.Rd | 1 33 files changed, 100 insertions(+), 79 deletions(-)
Title: Searching for Optimal MDS Procedure for Metric Data
Description: Selecting the optimal multidimensional scaling (MDS) procedure for metric data via metric MDS (ratio, interval, mspline) and nonmetric MDS (ordinal). Selecting the optimal MDS procedure for statistical data referring to the evaluation of tourist attractiveness of Lower Silesian counties (BORG I., GROENEN P.J.F., MAIR P., (2013) <doi:10.1007/978-3-642-31848-1>, DE LEEUW J., MAIR P., (2015) <doi:10.1002/9781118445112.stat06268.pub2>, WALESIAK M., (2016) <doi:10.15611/ekt.2016.2.01>).
Author: Marek Walesiak <marek.walesiak@ue.wroc.pl> Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Maintainer: Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Diff between mdsOpt versions 0.1-3 dated 2017-05-19 and 0.1-4 dated 2017-07-24
DESCRIPTION | 10 +-- MD5 | 12 ++-- R/optSmacofSym.r | 120 ++++++++++++++++++++++---------------------- man/data_lower_silesian.rd | 20 ++++--- man/findOptimalSmacofSym.rd | 30 +++++------ man/optSmacofSym_mMDS.rd | 48 +++++++++-------- man/optSmacofSym_nMDS.rd | 47 ++++++++--------- 7 files changed, 149 insertions(+), 138 deletions(-)
Title: Tool for Ensemble Feature Selection
Description: Provides a function to check the
importance of a feature based on a dependent classification
variable. An ensemble of feature selection methods
is used to determine the normalized importance value of
all features. Combining these methods in one function
(building the cumulative importance values) provides a
stable feature selection tool. This selection
can also be viewed in a barplot using the barplot_fs() function
and proved using the evaluation function efs_eval().
Author: Nikita Genze, Ursula Neumann
Maintainer: Ursula Neumann <u.neumann@wz-straubing.de>
Diff between EFS versions 1.0.1 dated 2016-11-17 and 1.0.3 dated 2017-07-24
DESCRIPTION | 13 +-- MD5 | 18 ++-- NAMESPACE | 64 ++++++++-------- R/barplot_fs.R | 49 +++++++++--- R/efs_eval.R | 161 ++++++++++++++++++++++++++++++++++-------- R/ensemble_fs.R | 32 +++++--- man/barplot_fs.Rd | 94 +++++++++++++----------- man/efs_eval.Rd | 200 ++++++++++++++++++++++++++++------------------------- man/efsdata.Rd | 67 ++++++++--------- man/ensemble_fs.Rd | 199 ++++++++++++++++++++++++++-------------------------- 10 files changed, 527 insertions(+), 370 deletions(-)
Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from
Model Outputs
Description: Compute marginal effects at the mean or average marginal effects from
statistical models and returns the result as tidy data frames. These
data frames are ready to use with the 'ggplot2'-package.
Marginal effects can be calculated for many different models. Interaction
terms, splines and polynomial terms are also supported. The two main
functions are 'ggpredict()' and 'ggaverage()', however, there are
some convenient wrapper-functions especially for polynomials or
interactions. There is a generic 'plot()'-method to plot the results
using 'ggplot2'.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between ggeffects versions 0.1.2 dated 2017-06-19 and 0.2.0 dated 2017-07-24
DESCRIPTION | 12 MD5 | 62 +- NAMESPACE | 6 NEWS.md | 20 R/emm.R |only R/getter.R | 24 R/ggalleffects.R | 32 - R/ggaverage.R | 324 ++++++------ R/ggeffect.R | 437 ++++++++--------- R/gginteraction.R | 595 +++++++++++------------ R/ggpoly.R | 290 +++++------ R/ggpredict.R | 739 +++++++++++++++------------- R/plot.R | 45 + R/predictions.R | 1074 +++++++++++++++++++++++------------------- R/utils.R | 185 +++---- R/utils_expand_data_to_grid.R | 277 +++++----- R/utils_handle_labels.R | 312 ++++++------ R/utils_link_inverse.R | 15 R/utils_model_family.R | 16 R/utils_model_frame.R | 20 R/utils_model_function.R | 10 README.md | 6 build/vignette.rds |binary inst/doc/marginaleffects.R | 11 inst/doc/marginaleffects.Rmd | 17 inst/doc/marginaleffects.html | 28 - man/emm.Rd |only man/ggeffect.Rd | 5 man/gginteraction.Rd | 5 man/ggpoly.Rd | 6 man/ggpredict.Rd | 51 + man/plot.Rd | 10 vignettes/marginaleffects.Rmd | 17 33 files changed, 2504 insertions(+), 2147 deletions(-)
Title: Animal Social Network Inference and Permutations for Ecologists
Description: Implements several tools that are used in animal social network analysis. In particular, this package provides the tools to infer groups and generate networks from observation data, perform permutation tests on the data, calculate lagged association rates, and performed multiple regression analysis on social network data.
Author: Damien R. Farine <dfarine@orn.mpg.de>
Maintainer: Damien R. Farine <dfarine@orn.mpg.de>
Diff between asnipe versions 1.1.3 dated 2017-02-21 and 1.1.4 dated 2017-07-24
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- man/asnipe-package.Rd | 4 ++-- man/get_network.Rd | 2 ++ 4 files changed, 12 insertions(+), 10 deletions(-)
Title: Spatial Uncertainty Propagation Analysis
Description: Uncertainty propagation analysis in spatial environmental modelling following methodology
described in Heuvelink et al. (2007) <doi:10.1080/13658810601063951>
and Brown and Heuvelink (2007) <doi:10.1016/j.cageo.2006.06.015>. The package provides functions
for examining the uncertainty propagation starting from input data and model parameters,
via the environmental model onto model outputs. The functions include uncertainty model specification,
stochastic simulation and propagation of uncertainty using Monte Carlo (MC) techniques.
Uncertain variables are described by probability distributions. Both numerical and categorical data types are handled.
Spatial auto-correlation within an attribute and cross-correlation between attributes is accommodated for.
The MC realizations may be used as input to the environmental models called from R, or externally.
Author: Kasia Sawicka [aut, cre],
Gerard Heuvelink [aut],
Dennis Walvoort [aut],
Stefan van Dam [ctb],
Damiano Luzzi [ctb]
Maintainer: Kasia Sawicka <kasia.sawicka@ed.ac.uk>
Diff between spup versions 0.1-0 dated 2017-04-13 and 0.1-1 dated 2017-07-24
spup-0.1-0/spup/inst/doc/CN.R |only spup-0.1-0/spup/inst/doc/CN.Rmd |only spup-0.1-0/spup/inst/doc/CN.html |only spup-0.1-0/spup/vignettes/CN.Rmd |only spup-0.1-0/spup/vignettes/examples/desktop.ini |only spup-0.1-1/spup/DESCRIPTION | 28 spup-0.1-1/spup/MD5 | 134 +- spup-0.1-1/spup/R/crm2vgm.R | 22 spup-0.1-1/spup/R/defineMUM.r | 6 spup-0.1-1/spup/R/genSample.JointNumericSpatial.R | 20 spup-0.1-1/spup/R/makecrm.R | 63 spup-0.1-1/spup/R/plot.SpatialCorrelogramModel.R | 7 spup-0.1-1/spup/README.md |only spup-0.1-1/spup/build/vignette.rds |binary spup-0.1-1/spup/data/OC.RData |binary spup-0.1-1/spup/data/OC_sd.RData |binary spup-0.1-1/spup/data/TN.RData |binary spup-0.1-1/spup/data/TN_sd.RData |binary spup-0.1-1/spup/data/dem30m.RData |binary spup-0.1-1/spup/data/dem30m_sd.RData |binary spup-0.1-1/spup/data/woon.RData |binary spup-0.1-1/spup/inst/doc/CN_v2.R |only spup-0.1-1/spup/inst/doc/CN_v2.Rmd |only spup-0.1-1/spup/inst/doc/CN_v2.html |only spup-0.1-1/spup/inst/doc/DEM_v3.Rmd | 10 spup-0.1-1/spup/inst/doc/DEM_v3.html | 791 ++++-------- spup-0.1-1/spup/inst/doc/ExternalModel_v2.Rmd | 3 spup-0.1-1/spup/inst/doc/ExternalModel_v2.html | 518 ++----- spup-0.1-1/spup/inst/doc/Rotterdam.Rmd | 3 spup-0.1-1/spup/inst/doc/Rotterdam.html | 489 ++----- spup-0.1-1/spup/man/OC.Rd | 1 spup-0.1-1/spup/man/OC_sd.Rd | 1 spup-0.1-1/spup/man/TN.Rd | 1 spup-0.1-1/spup/man/TN_sd.Rd | 1 spup-0.1-1/spup/man/check_distribution.Rd | 1 spup-0.1-1/spup/man/check_if_Spatial.Rd | 1 spup-0.1-1/spup/man/crm2vgm.Rd | 5 spup-0.1-1/spup/man/defineMUM.Rd | 7 spup-0.1-1/spup/man/defineUM.Rd | 1 spup-0.1-1/spup/man/dem30m.Rd | 1 spup-0.1-1/spup/man/dem30m_sd.Rd | 1 spup-0.1-1/spup/man/distribution_sampling.Rd | 1 spup-0.1-1/spup/man/distribution_sampling_raster.Rd | 1 spup-0.1-1/spup/man/executable.Rd | 1 spup-0.1-1/spup/man/find_strata.Rd | 1 spup-0.1-1/spup/man/genSample.JointNumericSpatial.Rd | 19 spup-0.1-1/spup/man/genSample.JointScalar.Rd | 1 spup-0.1-1/spup/man/genSample.MarginalCategoricalSpatial.Rd | 1 spup-0.1-1/spup/man/genSample.MarginalNumericSpatial.Rd | 1 spup-0.1-1/spup/man/genSample.MarginalScalar.Rd | 1 spup-0.1-1/spup/man/genSample.Rd | 1 spup-0.1-1/spup/man/list_depth.Rd | 1 spup-0.1-1/spup/man/makecrm.Rd | 20 spup-0.1-1/spup/man/mean_MC_sgdf.Rd | 1 spup-0.1-1/spup/man/plot.SpatialCorrelogramModel.Rd | 8 spup-0.1-1/spup/man/print.template.Rd | 1 spup-0.1-1/spup/man/propagate.Rd | 1 spup-0.1-1/spup/man/quantile_MC_sgdf.Rd | 1 spup-0.1-1/spup/man/render.Rd | 1 spup-0.1-1/spup/man/render.character.Rd | 1 spup-0.1-1/spup/man/render.template.Rd | 1 spup-0.1-1/spup/man/sd_MC_sgdf.Rd | 1 spup-0.1-1/spup/man/spup--pkg.Rd | 3 spup-0.1-1/spup/man/stratsamp.Rd | 1 spup-0.1-1/spup/man/template.Rd | 1 spup-0.1-1/spup/man/var_MC_sgdf.Rd | 1 spup-0.1-1/spup/man/varcov.Rd | 1 spup-0.1-1/spup/man/vgm2crm.Rd | 1 spup-0.1-1/spup/man/woon.Rd | 1 spup-0.1-1/spup/vignettes/CN_v2.Rmd |only spup-0.1-1/spup/vignettes/DEM_v3.Rmd | 10 spup-0.1-1/spup/vignettes/ExternalModel_v2.Rmd | 3 spup-0.1-1/spup/vignettes/Rotterdam.Rmd | 3 73 files changed, 814 insertions(+), 1391 deletions(-)
Title: Analyse Sentiment of English Sentences
Description: Analyses sentiment of a sentence in English and assigns score to it. It can classify sentences to the following categories of sentiments:- Positive, Negative, very Positive, very negative,
Neutral. For a vector of sentences, it counts the number of sentences in each
category of sentiment.In calculating the score, negation and various degrees
of adjectives are taken into consideration. It deals only with English sentences.
Author: Subhasree Bose <subhasree10.7@gmail.com> with contributons from Saptarsi Goswami.
Maintainer: Subhasree Bose <subhasree10.7@gmail.com>
Diff between RSentiment versions 2.1.6 dated 2017-07-20 and 2.2 dated 2017-07-24
DESCRIPTION | 6 ++-- MD5 | 14 ++++++--- NAMESPACE | 3 ++ R/custom.R |only R/test.R | 23 ++++++++-------- man/calculate_custom_score.Rd |only man/calculate_custom_sentiment.Rd |only man/calculate_custom_total_presence_sentiment.Rd |only tests/testthat/testing.R | 33 ++++++++++++++++++++++- vignettes/Introduction.Rmd | 8 ++++- 10 files changed, 66 insertions(+), 21 deletions(-)
Title: Multivariate Genomic Selection
Description: Estimating trait heritability and handling overfitting. This package includes a collection of functions for (1) estimating genetic variance-covariances and calculate trait heritability; and (2) handling overfitting by calculating the variance components and the heritability through cross validation.
Author: Zhenyu Jia
Maintainer: Zhenyu Jia <ajia.ucr@gmail.com>
Diff between GSMX versions 0.1 dated 2016-10-03 and 1.1 dated 2017-07-24
DESCRIPTION | 10 +-- MD5 | 12 ++-- NAMESPACE | 3 - R/gsm.R | 147 ++++++++++++++++++++++++++++++--------------------- data/pseudo.data.rda |binary man/GSMX-package.Rd | 6 +- man/pseudo.data.Rd | 2 7 files changed, 105 insertions(+), 75 deletions(-)
Title: Generalized Iterative Proportional Fitting for Relational Models
Description: Maximum likelihood estimation under relational models, with or without the overall effect.
Author: Anna Klimova, Tamas Rudas
Maintainer: Anna Klimova <aklimova25@gmail.com>
Diff between gIPFrm versions 2.0 dated 2014-03-20 and 3.1 dated 2017-07-24
DESCRIPTION | 10 +++--- MD5 | 16 +++++----- NAMESPACE | 1 R/bisection.update.R | 5 +-- R/g.ipf.R | 79 ++++++++++++++++++-------------------------------- R/grid.update.R | 5 +-- man/g.ipf.Rd | 10 +++++- man/gIPFrm-package.Rd | 11 +++++- man/ipf.gamma.Rd | 4 ++ 9 files changed, 70 insertions(+), 71 deletions(-)