Title: Methods for Visualization of Computer Experiments Design and
Surrogate
Description: View 2D/3D sections, contour plots, mesh of excursion sets for computer experiments designs, surrogates or test functions.
Author: Yann Richet, Yves Deville, Clement Chevalier
Maintainer: Yann Richet <yann.richet@irsn.fr>
Diff between DiceView versions 2.0-0 dated 2020-07-03 and 2.0-1 dated 2020-11-27
DESCRIPTION | 15 ++++++++------- MD5 | 13 +++++++------ NAMESPACE | 5 ----- R/mesh_set.R | 13 ++++--------- R/sectionview3d.fun.R | 13 +++++++------ R/sectionview3d.km.R | 12 ++++++------ R/sectionview3d.list.R | 11 ++++++----- R/wrapper3d.R |only 8 files changed, 38 insertions(+), 44 deletions(-)
Title: Transformation Boosting Machines
Description: Boosting the likelihood of conditional and shift transformation models as introduced in \doi{10.1007/s11222-019-09870-4}.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tbm versions 0.3-2.1 dated 2020-04-01 and 0.3-3 dated 2020-11-27
tbm-0.3-2.1/tbm/inst/simulations/plot_dgp.rda |only tbm-0.3-3/tbm/DESCRIPTION | 10 +++++----- tbm-0.3-3/tbm/MD5 | 24 ++++++++++++------------ tbm-0.3-3/tbm/build/vignette.rds |binary tbm-0.3-3/tbm/inst/NEWS.Rd | 8 ++++++++ tbm-0.3-3/tbm/inst/doc/tbm_supplement.R | 8 ++++---- tbm-0.3-3/tbm/inst/doc/tbm_supplement.Rnw | 8 ++++---- tbm-0.3-3/tbm/inst/doc/tbm_supplement.pdf |binary tbm-0.3-3/tbm/man/ctmboost.Rd | 6 +++--- tbm-0.3-3/tbm/man/stmboost.Rd | 6 +++--- tbm-0.3-3/tbm/tests/Rplots.pdf |only tbm-0.3-3/tbm/tests/bodyfat.R | 4 ++-- tbm-0.3-3/tbm/tests/bodyfat.Rout.save | 23 +++++++---------------- tbm-0.3-3/tbm/vignettes/tbm_supplement.Rnw | 8 ++++---- 14 files changed, 52 insertions(+), 53 deletions(-)
Title: 'GitHub' 'API'
Description: Minimal client to access the 'GitHub' 'API'.
Author: Gábor Csárdi [cre, ctb],
Jennifer Bryan [aut],
Hadley Wickham [aut],
RStudio [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between gh versions 1.1.0 dated 2020-01-24 and 1.2.0 dated 2020-11-27
gh-1.1.0/gh/R/package.R |only gh-1.1.0/gh/man/slugify_url.Rd |only gh-1.1.0/gh/tests/testthat/test-build_request.R |only gh-1.1.0/gh/tests/testthat/test-github_remote.R |only gh-1.1.0/gh/tests/testthat/test-mock-error.R |only gh-1.1.0/gh/tests/testthat/test-mock-whoami.R |only gh-1.1.0/gh/tests/testthat/test-na-null.R |only gh-1.1.0/gh/tests/testthat/test-token.R |only gh-1.2.0/gh/DESCRIPTION | 37 ++- gh-1.2.0/gh/LICENSE | 2 gh-1.2.0/gh/MD5 | 69 +++--- gh-1.2.0/gh/NAMESPACE | 6 gh-1.2.0/gh/NEWS.md | 42 +++- gh-1.2.0/gh/R/gh-package.R |only gh-1.2.0/gh/R/gh.R |only gh-1.2.0/gh/R/gh_gql.R | 7 gh-1.2.0/gh/R/gh_rate_limit.R |only gh-1.2.0/gh/R/gh_request.R | 121 ++++++++++- gh-1.2.0/gh/R/gh_response.R | 2 gh-1.2.0/gh/R/gh_token.R | 243 ++++++++---------------- gh-1.2.0/gh/R/gh_whoami.R | 12 - gh-1.2.0/gh/R/print.R | 2 gh-1.2.0/gh/R/utils.R | 3 gh-1.2.0/gh/README.md | 148 ++++++-------- gh-1.2.0/gh/build |only gh-1.2.0/gh/inst |only gh-1.2.0/gh/man/gh-package.Rd |only gh-1.2.0/gh/man/gh.Rd | 95 +++++---- gh-1.2.0/gh/man/gh_gql.Rd | 48 ---- gh-1.2.0/gh/man/gh_rate_limit.Rd |only gh-1.2.0/gh/man/gh_token.Rd | 123 +++--------- gh-1.2.0/gh/man/gh_whoami.Rd | 4 gh-1.2.0/gh/tests/testthat.R | 6 gh-1.2.0/gh/tests/testthat/helper-offline.R | 14 - gh-1.2.0/gh/tests/testthat/helper.R | 18 + gh-1.2.0/gh/tests/testthat/test-errors.R |only gh-1.2.0/gh/tests/testthat/test-gh_rate_limit.R |only gh-1.2.0/gh/tests/testthat/test-gh_request.R |only gh-1.2.0/gh/tests/testthat/test-gh_token.R |only gh-1.2.0/gh/tests/testthat/test-gh_whoami.R |only gh-1.2.0/gh/tests/testthat/test-git.R |only gh-1.2.0/gh/tests/testthat/test-mock-repos.R | 88 +++++--- gh-1.2.0/gh/tests/testthat/test-old-templates.R |only gh-1.2.0/gh/tests/testthat/test-spelling.R |only gh-1.2.0/gh/tests/testthat/test-utils.R | 45 ++++ gh-1.2.0/gh/vignettes |only 46 files changed, 587 insertions(+), 548 deletions(-)
Title: Locate Errors with Validation Rules
Description: Errors in data can be located and removed using validation rules from package 'validate'.
Author: Edwin de Jonge [aut, cre] (<https://orcid.org/0000-0002-6580-4718>),
Mark van der Loo [aut]
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between errorlocate versions 0.4 dated 2020-09-29 and 0.5.1 dated 2020-11-27
DESCRIPTION | 15 +-- MD5 | 75 ++++++++------- NAMESPACE | 1 NEWS.md | 19 +++ R/MipRules.R | 113 +++++++++++++++++++---- R/categorical.R | 25 ++++- R/conditional.R | 9 + R/dnf.R | 18 +++ R/errorlocalizer.R | 136 ++++++++++++++++++++++------ R/errorlocation.R | 31 +++++- R/inspect_mip.R |only R/linear.R | 37 +++++++ R/locate-errors.R | 1 R/log_extract.R |only R/mip_lpsolve.R | 9 + R/mip_rule.R | 19 +++ R/replace-errors.R | 5 - R/soft-rule.R | 27 ++++- build |only inst |only man/MipRules-class.Rd | 9 + man/errorlocation.Rd | 9 + man/errors_removed.Rd | 28 +++++ man/expect_values.Rd | 5 - man/inspect_mip.Rd |only man/is_categorical.Rd | 11 ++ man/is_conditional.Rd | 11 ++ man/is_linear.Rd | 11 ++ man/locate_errors.Rd | 8 + man/replace_errors.Rd | 10 +- tests/testthat/test-categorical.R | 6 + tests/testthat/test-errorlocalizer.R | 10 ++ tests/testthat/test-errorlocation-print.txt | 2 tests/testthat/test-errorlocation.R | 18 +++ tests/testthat/test-linear.R | 54 ++++++++++- tests/testthat/test-locate_errors.R | 87 +++++++++++++++++ tests/testthat/test-mip-lpsolve.R | 6 + tests/testthat/test-mip.R | 2 tests/testthat/test-soft-rule.R | 8 + vignettes |only 40 files changed, 715 insertions(+), 120 deletions(-)
Title: Analyze Shot Group Data
Description: Analyzes shooting data with respect to group shape,
precision, and accuracy. This includes graphical methods,
descriptive statistics, and inference tests using standard,
but also non-parametric and robust statistical methods.
Implements distributions for radial error in bivariate normal
variables. Works with files exported by 'OnTarget PC/TDS',
'Silver Mountain' e-target, 'ShotMarker' e-target, or 'Taran',
as well as with custom data files in text format.
Supports inference from range statistics like extreme spread.
Includes a set of web-based graphical user interfaces.
Author: Daniel Wollschlaeger
Maintainer: Daniel Wollschlaeger <dwoll@kuci.org>
Diff between shotGroups versions 0.7.5.1 dated 2019-07-14 and 0.7.5.2 dated 2020-11-27
DESCRIPTION | 8 +-- MD5 | 72 ++++++++++++++-------------- R/CEPs.R | 2 R/compareGroups.R | 6 +- R/groupShape.R | 5 + R/rayleigh.R | 22 ++++---- R/readData.R | 94 ++++++++++++++++++++++++------------- R/readDataSM.R | 91 +++++++++++++++++++---------------- build/vignette.rds |binary data/DF300BLK.rda |binary data/DF300BLKhl.rda |binary data/DFcciHV.rda |binary data/DFcm.rda |binary data/DFdistr.rda |binary data/DFinch.rda |binary data/DFlandy01.rda |binary data/DFlandy02.rda |binary data/DFlandy03.rda |binary data/DFlandy04.rda |binary data/DFlistCm.rda |binary data/DFsavage.rda |binary data/DFscar17.rda |binary data/DFtalon.rda |binary data/targets.rda |binary inst/ChangeLog | 6 ++ inst/doc/shotGroups.Rnw | 8 +-- inst/doc/shotGroups.pdf |binary inst/shotGroups_AnalyzeGroups/ui.R | 10 +-- man/DF300BLKhl.Rd | 2 man/DF300blk.Rd | 2 man/DFcciHV.Rd | 2 man/DFsavage.Rd | 2 man/DFscar17.Rd | 2 man/DFtalon.Rd | 2 man/shotGroups-package.Rd | 4 - vignettes/lit.bib | 28 +++++------ vignettes/shotGroups.Rnw | 8 +-- 37 files changed, 210 insertions(+), 166 deletions(-)
Title: Create Japanese Administration Area and Office Maps
Description: Utilizing the data that Japanese administration area provided
by the National Land Numerical Information download service (<https://nlftp.mlit.go.jp/ksj/index.html>).
This package provide map data is based on the Digital Map 25000 (Map Image) published
by Geospatial Information Authority of Japan (Approval No.603FY2017 information usage <https://www.gsi.go.jp>).
Author: Shinya Uryu [aut, cre] (<https://orcid.org/0000-0002-0493-6186>),
Geospatial Information Authority of Japan [dtc] (This package data
sets, National Land numerical information by the Geographical
Survey Institute with the approval of Geographical Survey Institute
Head (Approval No.603FY2017 information usage))
Maintainer: Shinya Uryu <suika1127@gmail.com>
Diff between jpndistrict versions 0.3.7 dated 2020-06-12 and 0.3.8 dated 2020-11-27
DESCRIPTION | 24 +++--- MD5 | 138 +++++++++++++++++++-------------------- NAMESPACE | 26 ------- NEWS.md | 4 + R/city_name_table.R | 13 +-- R/export_mesh.R | 52 ++++++++++---- R/find_city.R | 79 +++++++++------------- R/spdf_jpn.R | 73 +++++++++----------- R/util.R | 66 ++++++++---------- README.md | 2 data/jpnprefs.rda |binary data/prefecture_mesh.rda |binary inst/CITATION | 2 inst/extdata/citycode_sets.rds |binary inst/extdata/ksj_n03/pref_01.rds |binary inst/extdata/ksj_n03/pref_02.rds |binary inst/extdata/ksj_n03/pref_03.rds |binary inst/extdata/ksj_n03/pref_04.rds |binary inst/extdata/ksj_n03/pref_05.rds |binary inst/extdata/ksj_n03/pref_06.rds |binary inst/extdata/ksj_n03/pref_07.rds |binary inst/extdata/ksj_n03/pref_08.rds |binary inst/extdata/ksj_n03/pref_09.rds |binary inst/extdata/ksj_n03/pref_10.rds |binary inst/extdata/ksj_n03/pref_11.rds |binary inst/extdata/ksj_n03/pref_12.rds |binary inst/extdata/ksj_n03/pref_13.rds |binary inst/extdata/ksj_n03/pref_14.rds |binary inst/extdata/ksj_n03/pref_15.rds |binary inst/extdata/ksj_n03/pref_16.rds |binary inst/extdata/ksj_n03/pref_17.rds |binary inst/extdata/ksj_n03/pref_18.rds |binary inst/extdata/ksj_n03/pref_19.rds |binary inst/extdata/ksj_n03/pref_20.rds |binary inst/extdata/ksj_n03/pref_21.rds |binary inst/extdata/ksj_n03/pref_22.rds |binary inst/extdata/ksj_n03/pref_23.rds |binary inst/extdata/ksj_n03/pref_24.rds |binary inst/extdata/ksj_n03/pref_25.rds |binary inst/extdata/ksj_n03/pref_26.rds |binary inst/extdata/ksj_n03/pref_27.rds |binary inst/extdata/ksj_n03/pref_28.rds |binary inst/extdata/ksj_n03/pref_29.rds |binary inst/extdata/ksj_n03/pref_30.rds |binary inst/extdata/ksj_n03/pref_31.rds |binary inst/extdata/ksj_n03/pref_32.rds |binary inst/extdata/ksj_n03/pref_33.rds |binary inst/extdata/ksj_n03/pref_34.rds |binary inst/extdata/ksj_n03/pref_35.rds |binary inst/extdata/ksj_n03/pref_36.rds |binary inst/extdata/ksj_n03/pref_37.rds |binary inst/extdata/ksj_n03/pref_38.rds |binary inst/extdata/ksj_n03/pref_39.rds |binary inst/extdata/ksj_n03/pref_40.rds |binary inst/extdata/ksj_n03/pref_41.rds |binary inst/extdata/ksj_n03/pref_42.rds |binary inst/extdata/ksj_n03/pref_43.rds |binary inst/extdata/ksj_n03/pref_44.rds |binary inst/extdata/ksj_n03/pref_45.rds |binary inst/extdata/ksj_n03/pref_46.rds |binary inst/extdata/ksj_n03/pref_47.rds |binary man/find_city.Rd | 4 - man/find_jis_code.Rd | 17 ---- man/find_pref.Rd | 4 - man/find_prefs.Rd | 4 - man/jpn_admins.Rd | 2 man/jpn_pref.Rd | 3 man/mesh_district.Rd | 10 +- tests/testthat/test-export.R | 17 ++-- tests/testthat/test-find_city.R | 15 ++-- 70 files changed, 253 insertions(+), 302 deletions(-)
Title: 'RStudio' Addin for Quick Setup of ShinyDashboard Apps
Description: This 'RStudio' addin enables faster creation of the project structure and design of 'ShinyDashboard' apps. The graphical interface allows you to add certain code templates interactively. In addition to generating the basic project structure, the navigation in the app itself can also be defined or the app can be structured with modules.
Author: Leon Binder [cre, aut],
Bernhard Bauer [ctb],
Michael Scholz [ctb],
Bernhard Daffner [ctb],
Jörg Bauer [ctb]
Maintainer: Leon Binder <leon.binder@th-deg.de>
Diff between ShinyQuickStarter versions 1.0.1 dated 2020-11-23 and 1.0.2 dated 2020-11-27
DESCRIPTION | 10 MD5 | 18 NEWS.md | 10 R/ShinyQuickStarter-package.R | 9 R/functions.R | 10 R/server.R | 3077 +++++++++++++++++++-------------------- R/shinyQuickStarter.R | 23 R/ui.R | 1086 ++++++------- inst/rstudio/addins.dcf | 2 man/ShinyQuickStarter-package.Rd | 9 10 files changed, 2137 insertions(+), 2117 deletions(-)
More information about ShinyQuickStarter at CRAN
Permanent link
Title: Interface to the JavaScript Library 'amCharts 4'
Description: Creates JavaScript charts. The charts can be included in 'Shiny' apps and R markdown documents, or viewed from the R console and 'RStudio' viewer. Based on the JavaScript library 'amCharts 4' and the R packages 'htmlwidgets' and 'reactR'. Currently available types of chart are: vertical and horizontal bar chart, radial bar chart, stacked bar chart, vertical and horizontal Dumbbell chart, line chart, scatter chart, range area chart, gauge chart, and boxplot chart.
Author: Stéphane Laurent [aut, cre],
Antanas Marcelionis [ctb, cph] ('amCharts' library
(https://www.amcharts.com/)),
Terence Eden [ctb, cph] ('SuperTinyIcons' library
(https://github.com/edent/SuperTinyIcons/)),
Tom Alexander [ctb, cph] ('regression-js' library
(https://github.com/Tom-Alexander/regression-js))
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Diff between rAmCharts4 versions 1.1.0 dated 2020-10-31 and 1.2.0 dated 2020-11-27
DESCRIPTION | 8 MD5 | 46 + NAMESPACE | 2 NEWS.md | 9 R/amBarChart.R | 14 R/amBoxplotChart.R |only R/amDumbbellChart.R | 14 R/amHorizontalBarChart.R | 14 R/amHorizontalDumbbellChart.R | 14 R/amLineChart.R | 28 + R/amRangeAreaChart.R | 28 + R/amScatterChart.R | 28 + R/amStackedBarChart.R | 29 + R/internal.R | 36 + inst/htmlwidgets/amChart4.js | 919 +++++++++++++++++++++++++++++++-------- inst/htmlwidgets/amChart4.js.map | 2 man/amBarChart.Rd | 6 man/amBoxplotChart.Rd |only man/amDumbbellChart.Rd | 6 man/amHorizontalBarChart.Rd | 6 man/amHorizontalDumbbellChart.Rd | 6 man/amLineChart.Rd | 12 man/amRangeAreaChart.Rd | 12 man/amScatterChart.Rd | 12 man/amStackedBarChart.Rd | 12 25 files changed, 1055 insertions(+), 208 deletions(-)
Title: Material Management
Description: A set of functions, classes and methods for performing ABC and ABC/XYZ analyses, identifying overperforming, underperforming and constantly performing items, and plotting, analyzing as well as predicting the temporal development of items.
Author: Leon Binder [cre, aut],
Bernhard Bauer [aut],
Michael Scholz [aut]
Maintainer: Leon Binder <leon.binder@th-deg.de>
Diff between matman versions 1.1.1 dated 2020-11-23 and 1.1.2 dated 2020-11-27
matman-1.1.1/matman/R/launchApp.R |only matman-1.1.2/matman/DESCRIPTION | 8 +- matman-1.1.2/matman/MD5 | 20 +++--- matman-1.1.2/matman/NAMESPACE | 9 +++ matman-1.1.2/matman/NEWS.md | 5 + matman-1.1.2/matman/R/globals.R | 2 matman-1.1.2/matman/R/matman-package.R | 4 - matman-1.1.2/matman/R/matmanDemo.R |only matman-1.1.2/matman/R/shinyAppServer.R | 13 ++-- matman-1.1.2/matman/R/shinyAppUI.R | 86 ++++++++++++++---------------- matman-1.1.2/matman/man/matman-package.Rd | 2 matman-1.1.2/matman/man/matmanDemo.Rd | 39 +++++++------ 12 files changed, 102 insertions(+), 86 deletions(-)
Title: Bounded Memory Linear and Generalized Linear Models
Description: Regression for data too large to fit in memory.
Author: Thomas Lumley
Maintainer: Thomas Lumley <tlumley@u.washington.edu>
Diff between biglm versions 0.9-2 dated 2020-05-26 and 0.9-2.1 dated 2020-11-27
biglm-0.9-2.1/biglm/DESCRIPTION | 10 +++++----- biglm-0.9-2.1/biglm/MD5 | 9 ++++----- biglm-0.9-2.1/biglm/NAMESPACE | 2 ++ biglm-0.9-2.1/biglm/R/coef.bigqr.R | 2 +- biglm-0.9-2.1/biglm/R/odbc.R | 6 +++--- biglm-0.9-2/biglm/test |only 6 files changed, 15 insertions(+), 14 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-19 0.6.3
2019-02-28 0.6.2
2019-01-24 0.6.1
Title: Utilities for Quantiles
Description: Functions for unconditional and conditional quantiles. These
include methods for transformation-based quantile regression,
quantile-based measures of location, scale and shape, methods for quantiles
of discrete variables, quantile-based multiple imputation, restricted
quantile regression, and directional quantile classification. A vignette
is given in Geraci (2016, The R Journal) <doi:10.32614/RJ-2016-037> and
included in the package.
Author: Marco Geraci [aut, cph, cre] (<https://orcid.org/0000-0002-6311-8685>),
Alessio Farcomeni [ctb] (Contributions to midrq code,
<https://orcid.org/0000-0002-7104-5826>),
Cinzia Viroli [ctb] (Contributions to dqc code,
<https://orcid.org/0000-0002-3278-5266>)
Maintainer: Marco Geraci <marco.geraci@uniroma1.it>
Diff between Qtools versions 1.5.2 dated 2020-07-08 and 1.5.3 dated 2020-11-27
DESCRIPTION | 25 +++--- MD5 | 39 +++++----- NAMESPACE | 3 NEWS | 8 ++ R/Qtools.R | 177 +++++++++++++++++++++++++++++++++++++++++++++++++ R/RcppExports.R | 8 ++ build/vignette.rds |binary inst/doc/Qtools.R | 2 inst/doc/Qtools.html | 21 +++-- man/Qtools-internal.Rd | 5 + man/Qtools-package.Rd | 4 - man/cmidecdf.Rd | 2 man/dqc.Rd |only man/dqcControl.Rd |only man/midq2q.Rd | 2 man/midrq.Rd | 2 man/midrqControl.Rd | 2 man/print.dqc.Rd |only man/summary.midrq.Rd | 2 man/vcov.midrq.Rd | 2 src/Qtools.cpp | 114 +++++++++++++++++++++++++++++++ src/RcppExports.cpp | 39 ++++++++++ 22 files changed, 408 insertions(+), 49 deletions(-)
More information about iNZightRegression at CRAN
Permanent link
Title: API Client for Fantasy Football League Platforms
Description: Helps access various Fantasy Football APIs by handling authentication and
rate-limiting, forming appropriate calls, and returning tidy
dataframes which can be easily connected to other data sources.
Author: Tan Ho [aut, cre]
Maintainer: Tan Ho <tan@tanho.ca>
Diff between ffscrapr versions 1.1.0 dated 2020-11-16 and 1.2.0 dated 2020-11-27
ffscrapr-1.1.0/ffscrapr/R/generics.R |only ffscrapr-1.1.0/ffscrapr/R/helpers.R |only ffscrapr-1.1.0/ffscrapr/R/utils.R |only ffscrapr-1.1.0/ffscrapr/man/forget.Rd |only ffscrapr-1.2.0/ffscrapr/DESCRIPTION | 16 ffscrapr-1.2.0/ffscrapr/MD5 | 285 ++++++---- ffscrapr-1.2.0/ffscrapr/NAMESPACE | 22 ffscrapr-1.2.0/ffscrapr/NEWS.md | 23 ffscrapr-1.2.0/ffscrapr/R/0_cache.R |only ffscrapr-1.2.0/ffscrapr/R/0_generics.R |only ffscrapr-1.2.0/ffscrapr/R/0_helpers.R |only ffscrapr-1.2.0/ffscrapr/R/0_utils.R |only ffscrapr-1.2.0/ffscrapr/R/dp_import.R | 10 ffscrapr-1.2.0/ffscrapr/R/flea_api.R |only ffscrapr-1.2.0/ffscrapr/R/flea_connect.R |only ffscrapr-1.2.0/ffscrapr/R/flea_draft.R |only ffscrapr-1.2.0/ffscrapr/R/flea_draftpicks.R |only ffscrapr-1.2.0/ffscrapr/R/flea_franchises.R |only ffscrapr-1.2.0/ffscrapr/R/flea_league.R |only ffscrapr-1.2.0/ffscrapr/R/flea_players.R |only ffscrapr-1.2.0/ffscrapr/R/flea_playerscores.R |only ffscrapr-1.2.0/ffscrapr/R/flea_rosters.R |only ffscrapr-1.2.0/ffscrapr/R/flea_schedule.R |only ffscrapr-1.2.0/ffscrapr/R/flea_scoring.R |only ffscrapr-1.2.0/ffscrapr/R/flea_standings.R |only ffscrapr-1.2.0/ffscrapr/R/flea_starters.R |only ffscrapr-1.2.0/ffscrapr/R/flea_transactions.R |only ffscrapr-1.2.0/ffscrapr/R/flea_userleagues.R |only ffscrapr-1.2.0/ffscrapr/R/mfl_api.R | 2 ffscrapr-1.2.0/ffscrapr/R/mfl_playerscores.R | 3 ffscrapr-1.2.0/ffscrapr/R/mfl_schedule.R | 1 ffscrapr-1.2.0/ffscrapr/R/mfl_scoring.R | 12 ffscrapr-1.2.0/ffscrapr/R/mfl_userleagues.R | 4 ffscrapr-1.2.0/ffscrapr/R/sleeper_api.R | 23 ffscrapr-1.2.0/ffscrapr/R/sleeper_draftpicks.R | 2 ffscrapr-1.2.0/ffscrapr/R/sleeper_franchises.R | 2 ffscrapr-1.2.0/ffscrapr/R/sleeper_league.R | 6 ffscrapr-1.2.0/ffscrapr/R/sleeper_rosters.R | 4 ffscrapr-1.2.0/ffscrapr/R/sleeper_schedule.R | 2 ffscrapr-1.2.0/ffscrapr/R/sleeper_scoring.R | 2 ffscrapr-1.2.0/ffscrapr/R/sleeper_standings.R | 16 ffscrapr-1.2.0/ffscrapr/R/sleeper_starters.R | 2 ffscrapr-1.2.0/ffscrapr/R/sleeper_transactions.R | 214 ++++--- ffscrapr-1.2.0/ffscrapr/R/sleeper_userleagues.R | 15 ffscrapr-1.2.0/ffscrapr/R/zzz.R | 81 +- ffscrapr-1.2.0/ffscrapr/README.md | 36 - ffscrapr-1.2.0/ffscrapr/build/vignette.rds |binary ffscrapr-1.2.0/ffscrapr/inst/doc/ffscrapr_caching.R |only ffscrapr-1.2.0/ffscrapr/inst/doc/ffscrapr_caching.Rmd |only ffscrapr-1.2.0/ffscrapr/inst/doc/ffscrapr_caching.html |only ffscrapr-1.2.0/ffscrapr/inst/doc/fleaflicker_basics.R |only ffscrapr-1.2.0/ffscrapr/inst/doc/fleaflicker_basics.Rmd |only ffscrapr-1.2.0/ffscrapr/inst/doc/fleaflicker_basics.html |only ffscrapr-1.2.0/ffscrapr/inst/doc/fleaflicker_getendpoint.R |only ffscrapr-1.2.0/ffscrapr/inst/doc/fleaflicker_getendpoint.Rmd |only ffscrapr-1.2.0/ffscrapr/inst/doc/fleaflicker_getendpoint.html |only ffscrapr-1.2.0/ffscrapr/inst/doc/mfl_basics.R | 8 ffscrapr-1.2.0/ffscrapr/inst/doc/mfl_basics.Rmd | 21 ffscrapr-1.2.0/ffscrapr/inst/doc/mfl_basics.html | 276 ++++----- ffscrapr-1.2.0/ffscrapr/inst/doc/mfl_getendpoint.R | 7 ffscrapr-1.2.0/ffscrapr/inst/doc/mfl_getendpoint.Rmd | 19 ffscrapr-1.2.0/ffscrapr/inst/doc/mfl_getendpoint.html | 120 ++-- ffscrapr-1.2.0/ffscrapr/inst/doc/sleeper_basics.R | 10 ffscrapr-1.2.0/ffscrapr/inst/doc/sleeper_basics.Rmd | 12 ffscrapr-1.2.0/ffscrapr/inst/doc/sleeper_basics.html | 236 ++++---- ffscrapr-1.2.0/ffscrapr/inst/doc/sleeper_getendpoint.R | 10 ffscrapr-1.2.0/ffscrapr/inst/doc/sleeper_getendpoint.Rmd | 28 ffscrapr-1.2.0/ffscrapr/inst/doc/sleeper_getendpoint.html | 96 +-- ffscrapr-1.2.0/ffscrapr/man/dot-add_allplay.Rd |only ffscrapr-1.2.0/ffscrapr/man/dot-ff_clear_cache.Rd |only ffscrapr-1.2.0/ffscrapr/man/dot-fn_choose_season.Rd | 2 ffscrapr-1.2.0/ffscrapr/man/dot-fn_drop_nulls.Rd | 2 ffscrapr-1.2.0/ffscrapr/man/dot-fn_set_ratelimit.Rd | 2 ffscrapr-1.2.0/ffscrapr/man/dot-fn_set_useragent.Rd | 2 ffscrapr-1.2.0/ffscrapr/man/dp_values.Rd | 2 ffscrapr-1.2.0/ffscrapr/man/ff_connect.Rd | 3 ffscrapr-1.2.0/ffscrapr/man/ff_draft.Rd | 13 ffscrapr-1.2.0/ffscrapr/man/ff_draftpicks.Rd | 18 ffscrapr-1.2.0/ffscrapr/man/ff_franchises.Rd | 16 ffscrapr-1.2.0/ffscrapr/man/ff_league.Rd | 16 ffscrapr-1.2.0/ffscrapr/man/ff_playerscores.Rd | 23 ffscrapr-1.2.0/ffscrapr/man/ff_rosters.Rd | 15 ffscrapr-1.2.0/ffscrapr/man/ff_schedule.Rd | 20 ffscrapr-1.2.0/ffscrapr/man/ff_scoring.Rd | 16 ffscrapr-1.2.0/ffscrapr/man/ff_standings.Rd | 20 ffscrapr-1.2.0/ffscrapr/man/ff_starters.Rd | 16 ffscrapr-1.2.0/ffscrapr/man/ff_transactions.Rd | 18 ffscrapr-1.2.0/ffscrapr/man/ff_userleagues.Rd | 13 ffscrapr-1.2.0/ffscrapr/man/fleaflicker_connect.Rd |only ffscrapr-1.2.0/ffscrapr/man/fleaflicker_getendpoint.Rd |only ffscrapr-1.2.0/ffscrapr/man/fleaflicker_players.Rd |only ffscrapr-1.2.0/ffscrapr/man/fleaflicker_userleagues.Rd |only ffscrapr-1.2.0/ffscrapr/man/pipe.Rd | 6 ffscrapr-1.2.0/ffscrapr/man/sleeper_getendpoint.Rd | 2 ffscrapr-1.2.0/ffscrapr/tests/testthat/api.myfantasyleague.com/2019/export-279298.R 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ffscrapr-1.2.0/ffscrapr/tests/testthat/api.sleeper.app/v1/league/521379020332068864/rosters.R | 79 +- ffscrapr-1.2.0/ffscrapr/tests/testthat/api.sleeper.app/v1/league/521379020332068864/traded_picks.R | 79 +- ffscrapr-1.2.0/ffscrapr/tests/testthat/api.sleeper.app/v1/league/521379020332068864/users.R | 79 +- ffscrapr-1.2.0/ffscrapr/tests/testthat/api.sleeper.app/v1/league/522458773317046272.R | 79 +- ffscrapr-1.2.0/ffscrapr/tests/testthat/api.sleeper.app/v1/league/522458773317046272/drafts.R | 79 +- ffscrapr-1.2.0/ffscrapr/tests/testthat/api.sleeper.app/v1/league/522458773317046272/traded_picks.R | 79 +- ffscrapr-1.2.0/ffscrapr/tests/testthat/api.sleeper.app/v1/league/522458773317046272/transactions/1.R | 79 +- ffscrapr-1.2.0/ffscrapr/tests/testthat/api.sleeper.app/v1/league/522458773317046272/transactions/2.R | 79 +- ffscrapr-1.2.0/ffscrapr/tests/testthat/api.sleeper.app/v1/league/522458773317046272/transactions/3.R | 79 +- 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ffscrapr-1.2.0/ffscrapr/tests/testthat/test-ff_draft.R | 7 ffscrapr-1.2.0/ffscrapr/tests/testthat/test-ff_draftpicks.R | 12 ffscrapr-1.2.0/ffscrapr/tests/testthat/test-ff_franchises.R | 8 ffscrapr-1.2.0/ffscrapr/tests/testthat/test-ff_league.R | 6 ffscrapr-1.2.0/ffscrapr/tests/testthat/test-ff_playerscores.R | 6 ffscrapr-1.2.0/ffscrapr/tests/testthat/test-ff_rosters.R | 6 ffscrapr-1.2.0/ffscrapr/tests/testthat/test-ff_schedule.R | 7 ffscrapr-1.2.0/ffscrapr/tests/testthat/test-ff_scoring.R | 6 ffscrapr-1.2.0/ffscrapr/tests/testthat/test-ff_standings.R | 12 ffscrapr-1.2.0/ffscrapr/tests/testthat/test-ff_starters.R | 9 ffscrapr-1.2.0/ffscrapr/tests/testthat/test-ff_transactions.R | 12 ffscrapr-1.2.0/ffscrapr/tests/testthat/test-ff_userleagues.R | 15 ffscrapr-1.2.0/ffscrapr/tests/testthat/test-helpers.R | 2 ffscrapr-1.2.0/ffscrapr/tests/testthat/test-players.R |only ffscrapr-1.2.0/ffscrapr/tests/testthat/www.fleaflicker.com |only ffscrapr-1.2.0/ffscrapr/vignettes/ffscrapr_caching.Rmd |only ffscrapr-1.2.0/ffscrapr/vignettes/fleaflicker_basics.Rmd |only ffscrapr-1.2.0/ffscrapr/vignettes/fleaflicker_getendpoint.Rmd |only ffscrapr-1.2.0/ffscrapr/vignettes/mfl_basics.Rmd | 21 ffscrapr-1.2.0/ffscrapr/vignettes/mfl_getendpoint.Rmd | 19 ffscrapr-1.2.0/ffscrapr/vignettes/sleeper_basics.Rmd | 12 ffscrapr-1.2.0/ffscrapr/vignettes/sleeper_getendpoint.Rmd | 28 146 files changed, 2496 insertions(+), 1674 deletions(-)
Title: Data Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Data menu includes interfaces for loading, saving,
viewing, visualizing, summarizing, transforming, and combining data. It also
contains functionality to generate reproducible reports of the analyses
conducted in the application.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.data versions 1.3.10 dated 2020-08-07 and 1.3.12 dated 2020-11-27
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 6 ++++++ R/radiant.R | 18 +++++++----------- README.md | 13 ++++++++----- inst/app/radiant.R | 14 +++++++------- inst/app/tools/app/about.md | 13 ++++++++----- inst/app/tools/data/manage_ui.R | 20 ++++++++++---------- man/copy_all.Rd | 2 +- man/copy_from.Rd | 2 +- 10 files changed, 61 insertions(+), 53 deletions(-)
Title: Nonparametric Preprocessing for Parametric Causal Inference
Description: Selects matched samples of the original treated and
control groups with similar covariate distributions -- can be
used to match exactly on covariates, to match on propensity
scores, or perform a variety of other matching procedures. The
package also implements a series of recommendations offered in
Ho, Imai, King, and Stuart (2007) <DOI:10.1093/pan/mpl013>.
Author: Daniel Ho [aut] (<https://orcid.org/0000-0002-2195-5469>),
Kosuke Imai [aut] (<https://orcid.org/0000-0002-2748-1022>),
Gary King [aut] (<https://orcid.org/0000-0002-5327-7631>),
Elizabeth Stuart [aut] (<https://orcid.org/0000-0002-9042-8611>),
Alex Whitworth [ctb],
Noah Greifer [ctb, cre, aut] (<https://orcid.org/0000-0003-3067-7154>)
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between MatchIt versions 4.0.0 dated 2020-11-14 and 4.0.1 dated 2020-11-27
DESCRIPTION | 22 +++++--- MD5 | 73 +++++++++++++++------------- NEWS.md | 17 ++++-- R/RcppExports.R | 4 + R/aux_functions.R | 12 +--- R/match.qoi.R | 3 - R/matchit.R | 4 - R/matchit2_methods.R | 99 +++++++++++++++++++++++++++++++++------ R/weights.matrix.R | 25 +-------- build/MatchIt.pdf |binary build/partial.rdb |binary inst/doc/MatchIt.html | 8 +-- inst/doc/assessing-balance.html | 6 +- inst/doc/estimating-effects.Rmd | 4 + inst/doc/estimating-effects.html | 12 ++-- inst/doc/matching-methods.Rmd | 2 inst/doc/matching-methods.html | 5 - inst/doc/sampling-weights.html | 4 - man/add_s.weights.Rd | 4 - man/distance.Rd | 12 ++-- man/figures |only man/lalonde.Rd | 2 man/match.data.Rd | 6 +- man/matchit.Rd | 21 +++----- man/method_cem.Rd |only man/method_exact.Rd | 2 man/method_full.Rd | 8 +-- man/method_genetic.Rd | 8 +-- man/method_optimal.Rd | 8 +-- man/plot.matchit.Rd | 2 man/plot.summary.matchit.Rd | 2 man/summary.matchit.Rd | 2 src/RcppExports.cpp | 13 +++++ src/nnm.cpp | 14 +++-- src/pairdistC.cpp | 3 - src/weights_matrix.cpp |only vignettes/estimating-effects.Rmd | 4 + vignettes/matching-methods.Rmd | 2 38 files changed, 248 insertions(+), 165 deletions(-)
Title: Data Set and Helper Functions for Wind Farm Layout Optimization
Problems
Description: Provides a convenient data set, a set of helper functions, and a benchmark function for
economically (profit) driven wind farm layout optimization. This enables researchers in the field
of the NP-hard (non-deterministic polynomial-time hard) problem of wind farm layout optimization
to focus on their optimization methodology contribution and also provides a realistic benchmark
setting for comparability among contributions. See Croonenbroeck, Carsten & Hennecke, David (2020)
<doi:10.1016/j.energy.2020.119244>.
Author: Carsten Croonenbroeck [aut, cre],
David Hennecke [ctb]
Maintainer: Carsten Croonenbroeck <carsten.croonenbroeck@uni-rostock.de>
Diff between wflo versions 1.5 dated 2020-04-22 and 1.6 dated 2020-11-26
DESCRIPTION | 17 INDEX | 16 MD5 | 57 +- NAMESPACE | 6 NEWS | 16 R/Functions.R | 1292 +++++++++++++++++++++++++++++++++++++++++++--- R/zzz.R | 6 inst/CITATION |only inst/doc/wflo.R | 24 inst/doc/wflo.Rnw | 30 - inst/doc/wflo.pdf |binary man/AirDensity.Rd |only man/Area.Rd |only man/Cost.Rd | 5 man/FarmData.Rd | 5 man/FarmVars.Rd | 7 man/GK2Index.Rd |only man/GK2LonLat.Rd |only man/GaussWS.Rd |only man/GenerateGauss.Rd |only man/GetFarmFromLonLat.Rd |only man/Height.Rd |only man/Index2GK.Rd |only man/JensenTrapezoid.Rd | 9 man/LonLat2GK.Rd |only man/MosettiTurbineCost.Rd |only man/PairPenalty.Rd | 3 man/PartialJensen.Rd |only man/PointInPolygon.Rd | 4 man/Profit.Rd | 11 man/QuickGauss3D.Rd |only man/ShowWakePenalizers.Rd | 65 ++ man/SwitchProfile.Rd |only man/WindspeedHellmann.Rd |only man/WindspeedLog.Rd |only man/Yield.Rd | 9 vignettes/refs.bib | 45 + vignettes/wflo.Rnw | 30 - 38 files changed, 1472 insertions(+), 185 deletions(-)
Title: Partially Separable Quasi-Newton
Description: Provides quasi-Newton methods to minimize partially separable
functions. The methods are largely described by
Nocedal and Wright (2006) <doi:10.1007/978-0-387-40065-5>.
Author: Benjamin Christoffersen [cre, aut]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Diff between psqn versions 0.1.3 dated 2020-11-14 and 0.1.4 dated 2020-11-26
DESCRIPTION | 6 ++-- MD5 | 12 ++++----- inst/doc/psqn.html | 44 ++++++++++++++++----------------- inst/include/lp.h | 56 ++++++++++++++++++++++++++++++++++++++++++ inst/include/psqn.h | 50 +++++++++++++++++++++++++++++--------- src/r-api.cpp | 68 +++++++++++++++++++++++++++++++++------------------- src/test-lp.cpp | 26 +++++++++++++++++++ 7 files changed, 195 insertions(+), 67 deletions(-)
Title: A Collection of Models that Employ a Prior Distribution on
Partitions
Description: Provides functions that fit hierarchical Gaussian and probit ordinal models.
A (covariate dependent) product partition model is used as a prior.
If a covariate dependent product partition model is selected,
then all the options detailed in Page, G.L.; Quintana, F.A.; (2018)
<doi:10.1007/s11222-017-9777-z> are available. In addition, a function
that fits a Gaussian likelihood spatial product partition model that is
detailed in Page, G.L.; Quintana, F.A.; (2016) <doi:10.1214/15-BA971> is
also provided.
Author: Garritt L. Page [aut, cre, cph],
S. McKay Curtis [ctb, cph],
Radford M. Neal [ctb, cph]
Maintainer: Garritt L. Page <page@stat.byu.edu>
Diff between ppmSuite versions 0.1.0 dated 2020-11-23 and 0.1.1 dated 2020-11-26
DESCRIPTION | 6 +- MD5 | 20 +++--- src/Rutil.c | 106 ++++--------------------------------- src/init.c | 9 +-- src/matrix.c | 4 - src/mcmcloop.missing.c | 19 +++--- src/mcmcloop.ordinal.missing.pmx.c | 33 +++++------ src/mcmcloop.ordinal.ppmx.c | 14 ++-- src/mcmcloop.ppmx.c | 20 +++--- src/mcmcloop.sppm.c | 7 +- src/routine.rppmx.c | 4 - 11 files changed, 82 insertions(+), 160 deletions(-)
Title: Genetics and Independence Testing of Mixed Genetic Panels
Description: Developed to deal with multi-locus genotype data, this package is especially designed for those panel which include different type of markers. Basic genetic parameters like allele frequency, genotype frequency, heterozygosity and Hardy-Weinberg test of mixed genetic data can be obtained. In addition, a new test for mutual independence which is compatible for mixed genetic data is developed in this package.
Author: Bing Song
Maintainer: Bing Song <bingsong@my.unthsc.edu>
Diff between mixIndependR versions 0.4.0 dated 2020-11-25 and 0.4.2 dated 2020-11-26
DESCRIPTION | 12 +- MD5 | 33 +++-- NEWS.md | 12 ++ R/GenotypeFreq.R | 6 - R/mixexample-data.R |only data |only inst/doc/BasicGenetics.R | 43 +++---- inst/doc/BasicGenetics.Rmd | 59 ++++----- inst/doc/BasicGenetics.html | 154 ++------------------------ inst/doc/DistributionBuildingNComparison.R | 33 ++--- inst/doc/DistributionBuildingNComparison.Rmd | 33 ++--- inst/doc/DistributionBuildingNComparison.html | 40 +----- inst/doc/HypothesisTest.R | 35 +++-- inst/doc/HypothesisTest.Rmd | 35 +++-- inst/doc/HypothesisTest.html | 15 +- man/mixexample.Rd |only vignettes/BasicGenetics.Rmd | 59 ++++----- vignettes/DistributionBuildingNComparison.Rmd | 33 ++--- vignettes/HypothesisTest.Rmd | 35 +++-- 19 files changed, 256 insertions(+), 381 deletions(-)
Title: Statistics of Extremes
Description: Conducts inference in statistical models for extreme values (de Carvalho et al (2012), <doi:10.1080/03610926.2012.709905>; de Carvalho and Davison (2014), <10.1080/01621459.2013.872651>; Einmahl et al (2016), <doi:10.1111/rssb.12099>).
Author: Miguel de Carvalho [aut, cre],
Rodrigo Rubio [aut],
Vianey Palacios [aut],
Alejandro Jara [ctb],
Tim Hanson [ctb]
Maintainer: Miguel de Carvalho <miguel.decarvalho@ed.ac.uk>
Diff between extremis versions 1.0 dated 2020-11-20 and 1.2 dated 2020-11-26
DESCRIPTION | 6 +- MD5 | 16 +++--- R/cPTdensity.R | 81 ++++++++++++++++++++++++---------- R/cdensity.R | 2 man/cPTdensity.Rd | 18 +++---- src/PTudensitybetapmh.f | 109 +++++++++++++++++++++++------------------------ src/ToolsDistributions.f | 6 -- src/ToolsRfun.c | 10 ++++ src/init.c | 2 9 files changed, 142 insertions(+), 108 deletions(-)
Title: Clustering of Micro Panel Data
Description: Two-step feature-based clustering method designed for micro panel (longitudinal) data with the artificial panel data generator. See Sobisek, Stachova, Fojtik (2018) <arXiv:1807.05926>.
Author: Jan Fojtik [aut, cre],
Anna Grishko [aut],
Lukas Sobisek [aut, cph, rev]
Maintainer: Jan Fojtik <9afojtik@gmail.com>
Diff between CluMP versions 0.8 dated 2020-02-17 and 0.8.1 dated 2020-11-26
DESCRIPTION | 20 +- MD5 | 38 ++-- NAMESPACE | 1 NEWS.md | 6 R/Generate_Panel.R | 336 +++++++++++++++++++++--------------------- R/OptiNum.R | 349 ++++++++++++++++++++++---------------------- R/PanelPlot.R | 215 +++++++++++++-------------- R/clump.R | 300 +++++++++++++++++++------------------- R/clump_profiles.R | 393 +++++++++++++++++++++++++------------------------- R/clump_view.R | 271 +++++++++++++++++----------------- man/CluMP.Rd | 5 man/CluMP_profiles.Rd | 3 man/CluMP_view.Rd | 13 + man/GeneratePanel.Rd | 13 + man/OptiNum.Rd | 10 + man/PanelPlot.Rd | 15 + man/ParamCubic.Rd | 6 man/ParamExpon.Rd | 6 man/ParamLinear.Rd | 6 man/ParamQuadrat.Rd | 6 20 files changed, 1030 insertions(+), 982 deletions(-)
Title: User Friendly Bayesian Data Analysis for Psychology
Description: Contains several Bayesian models for data analysis of psychological tests. A user friendly interface for these models should enable students and researchers to perform professional level Bayesian data analysis without advanced knowledge in programming and Bayesian statistics. This package is based on the Stan platform (Carpenter et el. 2017 <doi:10.18637/jss.v076.i01>).
Author: Jure Demšar [cre, aut],
Grega Repovš [aut],
Erik Štrumbelj [aut],
Trustees of Columbia University [cph],
John Kruschke [cph] (R/shared_functions.R - mcmc_hdi,
src/stan_files/ttest.stan),
Rasmus Baath [cph] (R/b_bootstrap.R)
Maintainer: Jure Demšar <jure.demsar@fri.uni-lj.si>
Diff between bayes4psy versions 1.2.3 dated 2020-02-20 and 1.2.4 dated 2020-11-26
DESCRIPTION | 8 MD5 | 232 ++--- NAMESPACE | 2 NEWS.md | 47 - README.md | 2 build/vignette.rds |binary inst/doc/adaptation_level.R | 13 inst/doc/adaptation_level.Rmd | 13 inst/doc/adaptation_level.html | 279 ++---- inst/doc/afterimages.R | 5 inst/doc/afterimages.Rmd | 7 inst/doc/afterimages.html | 619 +++++---------- inst/doc/flanker.R | 10 inst/doc/flanker.Rmd | 10 inst/doc/flanker.html | 451 ++++------ inst/doc/stroop.R | 26 inst/doc/stroop.Rmd | 40 inst/doc/stroop.html | 348 ++------ man/b_bootstrap.Rd | 118 +- man/b_color.Rd | 228 ++--- man/b_linear.Rd | 154 +-- man/b_prior-class.Rd | 34 man/b_prior-get_prior_id.Rd | 34 man/b_reaction_time.Rd | 140 +-- man/b_results-class.Rd | 16 man/b_results-compare_distributions.Rd | 32 man/b_results-compare_means.Rd | 32 man/b_results-get_parameters.Rd | 26 man/b_results-get_subject_parameters.Rd | 26 man/b_results-plot_distributions.Rd | 32 man/b_results-plot_distributions_difference.Rd | 32 man/b_results-plot_fit.Rd | 32 man/b_results-plot_means.Rd | 30 man/b_results-plot_means_difference.Rd | 32 man/b_results-plot_trace.Rd | 26 man/b_success_rate.Rd | 130 +-- man/b_ttest.Rd | 126 +-- man/bayes4psy-datasets.Rd | 356 ++++---- man/bayes4psy-package.Rd | 30 man/color_class-class.Rd | 602 +++++++------- man/color_class-compare_distributions.Rd | 54 - man/color_class-compare_means.Rd | 54 - man/color_class-get_parameters.Rd | 50 - man/color_class-plot_distributions.Rd | 54 - man/color_class-plot_distributions_difference.Rd | 54 - man/color_class-plot_distributions_hsv.Rd | 60 - man/color_class-plot_fit.Rd | 54 - man/color_class-plot_fit_hsv.Rd | 56 - man/color_class-plot_hsv.Rd | 56 - man/color_class-plot_means.Rd | 54 - man/color_class-plot_means_difference.Rd | 54 - man/color_class-plot_means_hsv.Rd | 60 - man/color_class-plot_trace.Rd | 50 - man/linear_class-class.Rd | 326 +++---- man/linear_class-compare_distributions.Rd | 54 - man/linear_class-compare_means.Rd | 54 - man/linear_class-get_parameters.Rd | 50 - man/linear_class-get_subject_parameters.Rd | 50 - man/linear_class-plot_distributions.Rd | 54 - man/linear_class-plot_distributions_difference.Rd | 54 - man/linear_class-plot_fit.Rd | 54 - man/linear_class-plot_means.Rd | 54 - man/linear_class-plot_means_difference.Rd | 54 - man/linear_class-plot_trace.Rd | 50 - man/mcmc_hdi.Rd | 42 - man/plot-color_class-missing-method.Rd | 50 - man/plot-linear_class-missing-method.Rd | 50 - man/plot-reaction_time_class-missing-method.Rd | 50 - man/plot-success_rate_class-missing-method.Rd | 50 - man/plot-ttest_class-missing-method.Rd | 42 - man/reaction_time_class-class.Rd | 378 ++++----- man/reaction_time_class-compare_distributions.Rd | 54 - man/reaction_time_class-compare_means.Rd | 54 - man/reaction_time_class-get_parameters.Rd | 50 - man/reaction_time_class-get_subject_parameters.Rd | 50 - man/reaction_time_class-plot_distributions.Rd | 54 - man/reaction_time_class-plot_distributions_difference.Rd | 54 - man/reaction_time_class-plot_fit.Rd | 54 - man/reaction_time_class-plot_means.Rd | 54 - man/reaction_time_class-plot_means_difference.Rd | 54 - man/reaction_time_class-plot_trace.Rd | 50 - man/show-color_class-method.Rd | 42 - man/show-linear_class-method.Rd | 42 - man/show-reaction_time_class-method.Rd | 42 - man/show-success_rate_class-method.Rd | 42 - man/show-ttest_class-method.Rd | 42 - man/success_rate_class-class.Rd | 346 ++++---- man/success_rate_class-compare_distributions.Rd | 54 - man/success_rate_class-compare_means.Rd | 54 - man/success_rate_class-get_parameters.Rd | 50 - man/success_rate_class-get_subject_parameters.Rd | 50 - man/success_rate_class-plot_distributions.Rd | 54 - man/success_rate_class-plot_distributions_difference.Rd | 54 - man/success_rate_class-plot_fit.Rd | 54 - man/success_rate_class-plot_means.Rd | 54 - man/success_rate_class-plot_means_difference.Rd | 54 - man/success_rate_class-plot_trace.Rd | 50 - man/summary-color_class-method.Rd | 42 - man/summary-linear_class-method.Rd | 42 - man/summary-reaction_time_class-method.Rd | 42 - man/summary-success_rate_class-method.Rd | 42 - man/summary-ttest_class-method.Rd | 42 - man/ttest_class-class.Rd | 426 +++++----- man/ttest_class-compare_distributions.Rd | 54 - man/ttest_class-compare_means.Rd | 54 - man/ttest_class-get_parameters.Rd | 50 - man/ttest_class-plot_distributions.Rd | 54 - man/ttest_class-plot_distributions_difference.Rd | 54 - man/ttest_class-plot_fit.Rd | 50 - man/ttest_class-plot_means.Rd | 54 - man/ttest_class-plot_means_difference.Rd | 54 - man/ttest_class-plot_trace.Rd | 50 - tests/testthat/test_linear.R | 2 vignettes/adaptation_level.Rmd | 13 vignettes/afterimages.Rmd | 7 vignettes/flanker.Rmd | 10 vignettes/stroop.Rmd | 40 117 files changed, 4492 insertions(+), 4908 deletions(-)
Title: Distributed Representations of Words
Description: Learn vector representations of words by continuous bag of words and skip-gram implementations of the 'word2vec' algorithm.
The techniques are detailed in the paper "Distributed Representations of Words and Phrases and their Compositionality" by Mikolov et al. (2013), available at <arXiv:1310.4546>.
Author: Jan Wijffels [aut, cre, cph] (R wrapper),
BNOSAC [cph] (R wrapper),
Max Fomichev [ctb, cph] (Code in src/word2vec)
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between word2vec versions 0.3.2 dated 2020-10-10 and 0.3.3 dated 2020-11-26
DESCRIPTION | 6 MD5 | 16 +- NAMESPACE | 1 NEWS.md | 5 R/doc2vec.R | 2 R/utils.R |only man/read.word2vec.Rd | 84 ++++++------ man/txt_clean_word2vec.Rd |only man/word2vec.Rd | 312 +++++++++++++++++++++++----------------------- man/write.word2vec.Rd | 108 +++++++-------- 10 files changed, 271 insertions(+), 263 deletions(-)
Title: 'sf'-Based Interface to the 'HERE' REST APIs
Description: Interface to the 'HERE' REST APIs <https://developer.here.com/develop/rest-apis>:
(1) geocode and autosuggest addresses or reverse geocode POIs using the 'Geocoder' API;
(2) route directions, travel distance or time matrices and isolines using the 'Routing' API;
(3) request real-time traffic flow and incident information from the 'Traffic' API;
(4) find request public transport connections and nearby stations from the 'Public Transit' API;
(5) request intermodal routes using the 'Intermodal Routing' API;
(6) get weather forecasts, reports on current weather conditions, astronomical
information and alerts at a specific location from the 'Destination Weather' API.
Locations, routes and isolines are returned as 'sf' objects.
Author: Merlin Unterfinger [aut, cre] (<https://orcid.org/0000-0003-2020-2366>),
Daniel Possenriede [ctb] (<https://orcid.org/0000-0002-6738-9845>)
Maintainer: Merlin Unterfinger <info@munterfinger.ch>
Diff between hereR versions 0.5.1 dated 2020-10-20 and 0.5.2 dated 2020-11-26
DESCRIPTION | 6 MD5 | 30 +- NEWS.md | 11 R/geocode.R | 24 + R/sysdata.rda |binary R/utils.R | 9 build/vignette.rds |binary inst/doc/authentication.html | 266 -------------------- inst/doc/geocoder.html | 366 ++++----------------------- inst/doc/intermodal.html | 346 +++----------------------- inst/doc/routing.html | 448 +++++++-------------------------- inst/doc/traffic.html | 302 +--------------------- inst/doc/transit.html | 428 ++++++-------------------------- inst/doc/weather.html | 557 +++++++++++------------------------------- man/geocode.Rd | 12 tests/testthat/test-geocode.R | 3 16 files changed, 541 insertions(+), 2267 deletions(-)
Title: Hierarchical Bayesian Analysis of North American BBS Data
Description: The North American Breeding Bird Survey (BBS) is a long-running
program that seeks to monitor the status and trends of the breeding birds in
North America. Since its start in 1966, the BBS has accumulated over 50 years
of data for over 500 species of North American Birds. Given the temporal and
spatial structure of the data, hierarchical Bayesian models are used to assess
the status and trends of these 500+ species of birds. 'bbsBayes' allows you to perform
hierarchical Bayesian analysis of BBS data. You can run a full
model analysis for one or more species that you choose, or you can take
more control and specify how the data should be stratified, prepared
for 'JAGS', or modelled. The functions provided here allow you to replicate
analyses performed by the United State Geological Survey (USGS, see Link
and Sauer (2011) <doi:10.1525/auk.2010.09220>) and Canadian Wildlife Service
(CWS, see Smith and Edwards (2020) <doi:10.1101/2020.03.26.010215>).
Author: Brandon P.M. Edwards [aut, cre],
Adam C. Smith [aut]
Maintainer: Brandon P.M. Edwards <edwardsb@uoguelph.ca>
Diff between bbsBayes versions 2.3.4.2020 dated 2020-10-22 and 2.3.5.2020 dated 2020-11-26
DESCRIPTION | 8 MD5 | 8 R/prepare-jags-data.R | 2 R/stratify.R | 9 - README.md | 407 ++++++++++++++++++++++++++++---------------------- 5 files changed, 247 insertions(+), 187 deletions(-)
Title: Efficient Designs for Discrete Choice Experiments
Description: Generates efficient designs for discrete choice experiments based on the multinomial logit model, and individually adapted designs for the mixed multinomial logit model. The generated designs can be presented on screen and choice data can be gathered using a shiny application. Traets F, Sanchez G, and Vandebroek M (2020) <doi:10.18637/jss.v096.i03>.
Author: Frits Traets [aut, cre],
Daniel Gil [ctb]
Maintainer: Frits Traets <frits.traets@kuleuven.be>
Diff between idefix versions 0.4.3 dated 2020-04-07 and 1.0.1 dated 2020-11-26
DESCRIPTION | 8 ++++---- MD5 | 21 +++++++++++---------- R/CEA.R | 1 + R/efficiency_algorithms.R | 2 ++ R/idefix.R | 2 +- build/partial.rdb |binary inst/CITATION |only inst/REFERENCES.bib | 13 +++++++++++-- man/Modfed.Rd | 3 +++ man/SeqCEA.Rd | 2 ++ man/SeqMOD.Rd | 2 ++ man/idefix-package.Rd | 4 +++- 12 files changed, 40 insertions(+), 18 deletions(-)
More information about affinitymatrix at CRAN
Permanent link
Title: (Randomized) Quasi-Random Number Generators
Description: Functionality for generating (randomized) quasi-random numbers in
high dimensions.
Author: Marius Hofert [aut, cre],
Christiane Lemieux [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Diff between qrng versions 0.0-7 dated 2019-09-09 and 0.0-8 dated 2020-11-26
DESCRIPTION | 9 ++++++--- MD5 | 12 +++++++----- NAMESPACE | 1 + R/auxiliaries.R |only R/qrng.R | 1 + R/test_functions.R | 16 ++++++++++++++-- man/qrng.Rd | 14 +++++++------- man/to_array.Rd |only 8 files changed, 36 insertions(+), 17 deletions(-)
Title: Fetch Data from 'National Stock Exchange (India)'
Description: Fetch data related to stocks, index, futures & options from the
'NSE (National Stock Exchange, India)'. This package is community maintained
and is not officially supported by 'NSE'. The accuracy of data is only as
correct as provided on <https://www.nseindia.com>.
Author: Lokesh Kumar [aut],
Aravind Hebbali [aut, cre],
Lionel Pinto [ctb]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Diff between nse2r versions 0.1.2 dated 2020-06-18 and 0.1.3 dated 2020-11-26
DESCRIPTION | 6 MD5 | 8 NEWS.md | 6 R/nse-stock.R | 10 README.md | 2004 ++++++++++++++++++++++++++++++++-------------------------- 5 files changed, 1144 insertions(+), 890 deletions(-)
Title: Visualizing and Analyzing Animal Track Data
Description: Contains functions to access movement data stored in 'movebank.org'
as well as tools to visualize and statistically analyze animal movement data,
among others functions to calculate dynamic Brownian Bridge Movement Models.
Move helps addressing movement ecology questions.
Author: Bart Kranstauber [aut, cre],
Marco Smolla [aut],
Anne K Scharf [aut]
Maintainer: Bart Kranstauber <b.kranstauber@uva.nl>
Diff between move versions 4.0.4 dated 2020-09-12 and 4.0.6 dated 2020-11-26
DESCRIPTION | 6 MD5 | 18 +- R/WebImport.R | 4 build/vignette.rds |binary inst/doc/browseMovebank.R | 2 inst/doc/browseMovebank.Rmd | 2 inst/doc/browseMovebank.html | 6 inst/doc/move.html | 381 +++++++++++++++++++++---------------------- tests/testthat/test.web.R | 48 ++--- vignettes/browseMovebank.Rmd | 2 10 files changed, 240 insertions(+), 229 deletions(-)
Title: Markov Chains
Description: Computation of various Markovian models for categorical data
including homogeneous Markov chains of any order, MTD models, Hidden Markov
models, and Double Chain Markov Models.
Author: Ogier Maitre and Kevin Emery, with contributions from Oliver Buschor and Andre Berchtold
Maintainer: Andre Berchtold <andre.berchtold@unil.ch>
Diff between march versions 3.1 dated 2019-08-18 and 3.3.2 dated 2020-11-26
march-3.1/march/man/march.name-march.Dcmm-method.Rd |only march-3.1/march/man/march.name-march.Indep-method.Rd |only march-3.1/march/man/march.name-march.Mc-method.Rd |only march-3.1/march/man/march.name-march.Mtd-method.Rd |only march-3.1/march/man/march.name.Rd |only march-3.1/march/man/march.thompson-march.Dcmm-numeric-method.Rd |only march-3.1/march/man/march.thompson-march.Indep-numeric-method.Rd |only march-3.1/march/man/march.thompson-march.Mc-numeric-method.Rd |only march-3.1/march/man/march.thompson-march.Mtd-numeric-method.Rd |only march-3.1/march/man/march.thompson.Rd |only march-3.3.2/march/DESCRIPTION | 19 march-3.3.2/march/MD5 | 91 march-3.3.2/march/NAMESPACE | 9 march-3.3.2/march/R/march.AllGenerics.R | 1496 ++++++---- march-3.3.2/march/R/march.ci.R | 70 march-3.3.2/march/R/march.dcmm.R | 13 march-3.3.2/march/R/march.dcmm.em.R | 21 march-3.3.2/march/R/march.diagnostic.R | 90 march-3.3.2/march/R/march.mtd.R | 84 march-3.3.2/march/data/Employment.2.rda |only march-3.3.2/march/data/pewee.rda |binary march-3.3.2/march/data/pewee_df.rda |binary march-3.3.2/march/data/sleep.rda |binary march-3.3.2/march/data/sleep_df.rda |binary march-3.3.2/march/man/Employment.2.Rd |only march-3.3.2/march/man/march.AIC.Rd | 64 march-3.3.2/march/man/march.BIC.Rd | 52 march-3.3.2/march/man/march.Dataset-class.Rd | 68 march-3.3.2/march/man/march.Dcmm-class.Rd | 74 march-3.3.2/march/man/march.Indep-class.Rd | 46 march-3.3.2/march/man/march.Mc-class.Rd | 50 march-3.3.2/march/man/march.Model-class.Rd | 44 march-3.3.2/march/man/march.Mtd-class.Rd | 66 march-3.3.2/march/man/march.Rd | 2 march-3.3.2/march/man/march.dataset.loadFromDataFrame.Rd | 145 march-3.3.2/march/man/march.dataset.loadFromFile.Rd | 61 march-3.3.2/march/man/march.dcmm.construct.Rd | 201 - march-3.3.2/march/man/march.dcmm.viterbi.Rd | 56 march-3.3.2/march/man/march.indep.bailey.Rd |only march-3.3.2/march/man/march.indep.construct.Rd | 64 march-3.3.2/march/man/march.indep.thompson.Rd |only march-3.3.2/march/man/march.mc.bailey.Rd |only march-3.3.2/march/man/march.mc.construct.Rd | 72 march-3.3.2/march/man/march.mc.thompson.Rd |only march-3.3.2/march/man/march.mtd.bailey.Rd |only march-3.3.2/march/man/march.mtd.construct.Rd | 113 march-3.3.2/march/man/march.mtd.thompson.Rd |only march-3.3.2/march/man/march.write.Rd | 42 march-3.3.2/march/man/pewee.Rd | 2 march-3.3.2/march/man/pewee_df.Rd | 2 march-3.3.2/march/man/pewee_t.Rd | 2 march-3.3.2/march/man/sleep.Rd | 2 march-3.3.2/march/man/sleep_df.Rd | 2 march-3.3.2/march/tests/examples/march.bailey.example.R |only march-3.3.2/march/tests/examples/march.dcmm.construct.example.R | 4 march-3.3.2/march/tests/examples/march.thompson.example.R | 4 56 files changed, 1830 insertions(+), 1301 deletions(-)
Title: Analyzing Data with Cellwise Outliers
Description: Tools for detecting cellwise outliers and robust methods to analyze
data which may contain them. Contains the implementation of the algorithms described in
Rousseeuw and Van den Bossche (2018) <doi:10.1080/00401706.2017.1340909> (open access)
Hubert et al. (2019) <doi:10.1080/00401706.2018.1562989> (open access),
Raymaekers and Rousseeuw (2019) <doi:10.1080/00401706.2019.1677270> (open access),
Raymaekers and Rousseeuw (2020) <arXiv:2005.07946> (open access),
Raymaekers and Rousseeuw (2020) <arXiv:1912.12446> (open access).
Examples can be found in the vignettes:
"DDC_examples", "MacroPCA_examples", "wrap_examples" and "transfo_examples".
Author: Jakob Raymaekers [aut, cre],
Peter Rousseeuw [aut],
Wannes Van den Bossche [ctb],
Mia Hubert [ctb]
Maintainer: Jakob Raymaekers <jakob.raymaekers@kuleuven.be>
Diff between cellWise versions 2.2.1 dated 2020-11-11 and 2.2.2 dated 2020-11-26
cellWise-2.2.1/cellWise/inst/doc/Wrap_examples.R |only cellWise-2.2.1/cellWise/inst/doc/Wrap_examples.Rmd |only cellWise-2.2.1/cellWise/inst/doc/Wrap_examples.html |only cellWise-2.2.1/cellWise/vignettes/Wrap_examples.Rmd |only cellWise-2.2.2/cellWise/DESCRIPTION | 15 cellWise-2.2.2/cellWise/MD5 | 27 - cellWise-2.2.2/cellWise/NAMESPACE | 7 cellWise-2.2.2/cellWise/R/RcppExports.R | 4 cellWise-2.2.2/cellWise/R/TVCN.R | 2 cellWise-2.2.2/cellWise/R/cellHandler.R |only cellWise-2.2.2/cellWise/build/vignette.rds |binary cellWise-2.2.2/cellWise/inst/doc/wrap_examples.R |only cellWise-2.2.2/cellWise/inst/doc/wrap_examples.Rmd |only cellWise-2.2.2/cellWise/inst/doc/wrap_examples.html |only cellWise-2.2.2/cellWise/man/DI.Rd |only cellWise-2.2.2/cellWise/man/cellHandler.Rd |only cellWise-2.2.2/cellWise/man/transfo.Rd | 2 cellWise-2.2.2/cellWise/src/Main.cpp | 423 +++++++++++++++++++- cellWise-2.2.2/cellWise/src/RcppExports.cpp | 16 cellWise-2.2.2/cellWise/vignettes/wrap_examples.Rmd |only 20 files changed, 454 insertions(+), 42 deletions(-)
Title: Modelling of Microbial Growth
Description: Modelling of microbial growth under isothermal and dynamic conditions.
Includes functions for model fitting and making prediction under isothermal and
dynamic conditions using methods (algorithms & models) common in
predictive microbiology (See Perez-Rodriguez and Valero (2012, ISBN:978-1-4614-5519-6)).
Author: Alberto Garre [aut, cre] (<https://orcid.org/0000-0002-4404-3550>),
Jeroen Koomen [aut],
Heidy den Besten [aut],
Marcel Zwietering [aut]
Maintainer: Alberto Garre <garre.alberto@gmail.com>
Diff between biogrowth versions 0.1.1 dated 2020-11-11 and 0.1.2 dated 2020-11-26
biogrowth-0.1.1/biogrowth/R/S3_plotting.R |only biogrowth-0.1.1/biogrowth/man/plot.DynamicGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/plot.FitDynamicGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/plot.FitDynamicGrowthMCMC.Rd |only biogrowth-0.1.1/biogrowth/man/plot.FitIsoGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/plot.FitMultipleDynamicGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/plot.FitMultipleGrowthMCMC.Rd |only biogrowth-0.1.1/biogrowth/man/plot.FitSecondaryGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/plot.IsothermalGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/plot.MCMCgrowth.Rd |only biogrowth-0.1.1/biogrowth/man/plot.StochasticGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/plot.TimeDistribution.Rd |only biogrowth-0.1.1/biogrowth/man/residuals.FitDynamicGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/residuals.FitDynamicGrowthMCMC.Rd |only biogrowth-0.1.1/biogrowth/man/residuals.FitIsoGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/residuals.FitMultipleDynamicGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/residuals.FitMultipleGrowthMCMC.Rd |only biogrowth-0.1.1/biogrowth/man/residuals.FitSecondaryGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/summary.FitDynamicGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/summary.FitDynamicGrowthMCMC.Rd |only biogrowth-0.1.1/biogrowth/man/summary.FitIsoGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/summary.FitMultipleDynamicGrowth.Rd |only biogrowth-0.1.1/biogrowth/man/summary.FitMultipleGrowthMCMC.Rd |only biogrowth-0.1.1/biogrowth/man/summary.FitSecondaryGrowth.Rd |only biogrowth-0.1.2/biogrowth/DESCRIPTION | 8 biogrowth-0.1.2/biogrowth/MD5 | 157 biogrowth-0.1.2/biogrowth/NAMESPACE | 235 biogrowth-0.1.2/biogrowth/NEWS.md | 45 biogrowth-0.1.2/biogrowth/R/DynamicGrowth_class.R |only biogrowth-0.1.2/biogrowth/R/FitDynamicGrowthMCMC_class.R |only biogrowth-0.1.2/biogrowth/R/FitDynamicGrowth_class.R |only biogrowth-0.1.2/biogrowth/R/FitIsoGrowth_class.R |only biogrowth-0.1.2/biogrowth/R/FitMultipleDynamicGrowth_class.R |only biogrowth-0.1.2/biogrowth/R/FitMultipleGrowthMCMC_class.R |only biogrowth-0.1.2/biogrowth/R/FitSecondaryGrowth_class.R |only biogrowth-0.1.2/biogrowth/R/IsothermalGrowth_class.R |only biogrowth-0.1.2/biogrowth/R/MCMCgrowth_class.R |only biogrowth-0.1.2/biogrowth/R/S3_methods.R | 474 - 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Title: Small Example Response and Response Time Data from PISA 2018
Description: Scored responses and responses times from the Canadian subsample of the PISA 2018 assessment, accessible as the "Cognitive Item Data File" by OECD (2019) <https://www.oecd.org/pisa/data/2018database/>.
Author: Benjamin Becker [aut, cre],
Esther Ulitzsch [ctb],
Christoph Koenig [ctb]
Maintainer: Benjamin Becker <b.becker@iqb.hu-berlin.de>
Diff between pisaRT versions 1.0.0 dated 2020-07-01 and 2.0.0 dated 2020-11-26
DESCRIPTION | 12 ++++----- MD5 | 25 ++++++++++---------- NAMESPACE | 4 +-- NEWS.md |only R/pisaL.R | 6 +++- R/pisaRT-package.R | 10 ++++---- R/pisaW.R | 6 +++- README.md | 9 +++---- data/pisaL.rda |binary data/pisaW.rda |binary man/pisaL.Rd | 56 +++++++++++++++++++++++---------------------- man/pisaRT.Rd | 50 ++++++++++++++++++++-------------------- man/pisaW.Rd | 54 ++++++++++++++++++++++--------------------- tests/testthat/test_pisa.R | 27 ++++++++++++++++++--- 14 files changed, 145 insertions(+), 114 deletions(-)
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 1.0.0 dated 2020-11-01 and 1.0.1 dated 2020-11-26
DESCRIPTION | 8 +-- MD5 | 10 +-- NEWS.md | 5 + R/forestglm.R | 14 ++--- build/vignette.rds |binary inst/doc/jstable.html | 130 ++++++++++++++++++++------------------------------ 6 files changed, 74 insertions(+), 93 deletions(-)
Title: Imputation of Count Data using Side Information
Description: Analysis, imputation, and multiple imputation of count data using covariates. LORI uses a log-linear model where main row and column effects are decomposed as regression terms on known covariates. A residual low-rank interaction term is also fitted. LORI returns estimates of covariate effects and interactions, as well as an imputed count table. The package also contains a multiple imputation procedure.
Author: Genevieve Robin [aut, cre]
Maintainer: Genevieve Robin <genevieve.robin@polytechnique.edu>
Diff between lori versions 2.2.0 dated 2019-12-10 and 2.2.1 dated 2020-11-26
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- NAMESPACE | 1 + R/altmin.R | 32 ++++++++++++++++---------------- R/cv.lori.R | 15 +++++++++------ R/lori.R | 9 ++++++--- R/mcgd.R | 10 +++++----- man/cv.lori.Rd | 21 ++++++++++++++++++--- man/lori.Rd | 20 +++++++++++++++++--- man/mi.lori.Rd | 19 +++++++++++++++---- 10 files changed, 102 insertions(+), 55 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-12-19 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-11 0.15
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-07 2.4
2014-07-21 2.3
2012-08-22 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-01-01 1.4
2013-06-18 1.3
2013-02-04 1.2
2012-09-26 1.1
2012-08-22 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-04-09 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-12-14 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-08-02 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-03-04 0.11
2017-02-28 0.10
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-08-16 1.01
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-12 3.0.0
2020-04-19 2.6.1
2020-01-20 2.6.0
2019-07-30 2.5.1
2019-07-01 2.5.0
2019-04-07 2.4.5
2019-03-18 2.4.4
2018-09-11 2.4.3
2018-03-11 2.4.2
2017-10-16 2.4.1
2017-06-06 2.4
2016-08-23 2.3
2016-02-25 2.2
2015-03-20 2.1
2014-11-18 2.0
2012-11-28 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-08-26 0.1-41
Title: Row by Row Data Processing Tool, Using 'DataSailr' Script
Description: A row by row data processing tool. You can write data processing code in 'DataSailr' script which is specially intended for data manipulation. The package uses 'libsailr' (C/C++ library) for its 'DataSailr' code parsing and its execution.
Author: Toshihiro Umehara [aut, cre],
Troy Hanson [cph, ctb] (uthash),
Howard Hinnant [cph, ctb] (date.h),
Adrian Colomitchi [cph, ctb] (date.h),
Florian Dang [cph, ctb] (date.h),
Paul Thompson [cph, ctb] (date.h),
Tomasz Kamiński [cph, ctb] (date.h),
Nemanja Trifunovic [cph, ctb] (utfcpp),
Kim Grasman [cph, ctb] (getopt_port),
Jon Clayden [cph, ctb] (ore package),
K.Kosako [cph, ctb] (onigmo author),
K.Takata [cph, ctb] (onigmo author),
Byte [cph, ctb] (onigmo contributor),
KUBO Takehiro [cph, ctb] (onigmo contributor),
Free Software Foundation, Inc [cph],
X Consortium [cph]
Maintainer: Toshihiro Umehara <toshi@niceume.com>
Diff between datasailr versions 0.8.6 dated 2020-08-26 and 0.8.7 dated 2020-11-26
DESCRIPTION | 12 +++--- MD5 | 36 +++++++++---------- NEWS.md | 13 +++++++ R/data_sailr_main.R | 27 ++++++++++---- README.md | 78 ++++++++++++++++++++++-------------------- configure | 61 +++++++++++++++++++++++++++----- configure.ac | 27 +++++++++++++- man/datasailr-package.Rd | 6 +-- man/sail.Rd | 12 +++--- src/Makevars.in | 10 ++--- src/Onigmo/Makefile.in | 9 ++-- src/Onigmo/aclocal.m4 | 36 +++++++++++++++++++ src/Onigmo/configure | 34 ++++++++++++++++++ src/Onigmo/configure.ac | 1 src/Onigmo/sample/Makefile.in | 7 ++- src/data_sailr_cpp_main.cpp | 1 src/libsailr/HISTORY.md | 6 +++ src/libsailr/tree_free.c | 5 ++ src/libsailr/vm/vm.c | 16 +++++--- 19 files changed, 291 insertions(+), 106 deletions(-)
Title: Efficient Computation of Ordinary and Generalized Poisson
Binomial Distributions
Description: Efficient implementations of multiple exact and approximate methods as described in Hong (2013) <doi:10.1016/j.csda.2012.10.006>, Biscarri, Zhao & Brunner (2018) <doi:10.1016/j.csda.2018.01.007> and Zhang, Hong & Balakrishnan (2018) <doi:10.1080/00949655.2018.1440294> for computing the probability mass, cumulative distribution and quantile functions, as well as generating random numbers for both the ordinary and generalized Poisson binomial distribution.
Author: Florian Junge [aut, cre]
Maintainer: Florian Junge <florian.junge@h-da.de>
Diff between PoissonBinomial versions 1.2.0 dated 2020-11-25 and 1.2.1 dated 2020-11-26
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 15 +++++++++++++-- inst/doc/proc_approx.html | 22 +++++++++++----------- inst/doc/proc_exact.html | 14 +++++++------- src/PoissonBinomial.cpp | 16 ++++++++-------- 6 files changed, 48 insertions(+), 37 deletions(-)
More information about PoissonBinomial at CRAN
Permanent link
Title: Bayesian Model Selection and Averaging for Non-Local and Local
Priors
Description: Bayesian model selection and averaging for regression and mixtures for non-local and selected local priors.
Author: David Rossell, John D. Cook, Donatello Telesca, P. Roebuck, Oriol Abril
Maintainer: David Rossell <rosselldavid@gmail.com>
Diff between mombf versions 2.2.9 dated 2019-12-06 and 3.0.1 dated 2020-11-26
ChangeLog | 18 DESCRIPTION | 8 MD5 | 63 - R/bms_ortho.R | 8 R/emomLM.R | 10 R/greedyGLM.R | 2 R/modelSelection.R | 390 +++++- R/modelSelectionGLM.R | 23 R/modelsearch.R | 3 R/msPriorSpec.R | 76 - R/nlpMarginal.R | 28 R/pmomLM.R | 4 R/pmomPM.R | 14 build/vignette.rds |binary data/hald.rda |binary inst/doc/mombf.pdf |binary man/modelSelection.Rd | 50 man/msPriorSpec-class.Rd | 37 man/nlpMarginals.Rd | 17 src/RcppExports.cpp | 16 src/cstat.cpp | 2 src/glm.cpp |only src/glm.h |only src/modelSel.cpp | 1773 +++++++++++++++++++++++------ src/modelSel.h | 133 +- src/modselFunction.cpp | 377 ++++++ src/modselFunction.h | 64 - src/nlpMarg.cpp | 38 src/nlpMarg.h | 4 tests/testthat/data-for-tests.R | 1 tests/testthat/test-modelSelection-enum.R | 31 tests/testthat/test-modelSelection-gibbs.R | 20 tests/testthat/test-mspriorspec.R |only tests/testthat/test-nlpMarginal-groups.R | 17 34 files changed, 2619 insertions(+), 608 deletions(-)
Title: Media News Extraction for Text Analysis
Description: Extract textual data from different media channels
through its source based on users choice of keywords.
These data can be used to perform text analysis to
identify patterns in respective media reporting.
The media channels used in this package are print media.
The data (or news) used are publicly available to consumers.
Author: Vatsal Aima [aut, cre]
Maintainer: Vatsal Aima <vaima75@hotmail.com>
Diff between MediaNews versions 0.2.0 dated 2020-11-24 and 0.2.1 dated 2020-11-26
DESCRIPTION | 20 ++++++++++---------- MD5 | 13 ++++++++----- NAMESPACE | 2 ++ R/TOI_News_Articles.R | 8 ++++++-- R/TOI_News_Dataset.R | 1 + R/emoji_Data.R |only README.md | 4 +++- data |only man/emoji_Data.Rd |only 9 files changed, 30 insertions(+), 18 deletions(-)
Title: Convert Between R Objects and Geometric Structures
Description: Geometry shapes in 'R' are typically represented by matrices (points, lines), with more complex
shapes being lists of matrices (polygons). 'Geometries' will convert various 'R' objects into these shapes.
Conversion functions are available at both the 'R' level, and through 'Rcpp'.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <david.cooley.au@gmail.com>
Diff between geometries versions 0.1.0 dated 2020-08-14 and 0.2.0 dated 2020-11-26
DESCRIPTION | 12 +- MD5 | 59 ++++++----- NEWS.md |only R/RcppExports.R | 20 ++- R/geometries.R | 6 - README.md | 92 +++++++++++++++++- build/vignette.rds |binary inst/doc/geometries.html | 64 ++++++++++++ inst/include/geometries/coordinates/dimensions.hpp | 69 ++++++------- inst/include/geometries/geometries.hpp | 17 +-- inst/include/geometries/nest/nest.hpp | 104 ++++++++++---------- inst/include/geometries/utils/close/close.hpp | 28 ++++- inst/include/geometries/utils/columns/columns.hpp | 41 ++++---- inst/include/geometries/utils/reshape |only inst/include/geometries/utils/sexp/sexp.hpp | 21 +++- inst/include/geometries/utils/split/split.hpp | 65 +++++++++--- inst/include/geometries/utils/vectors/vectors.hpp | 82 +++++++--------- inst/tinytest/test_attributes.R | 50 +++++++++ inst/tinytest/test_columns.R | 5 inst/tinytest/test_coordinates.R | 39 +++++-- inst/tinytest/test_geometries.R | 4 inst/tinytest/test_nest.R | 106 ++++++++++----------- inst/tinytest/test_sexp.R | 2 inst/tinytest/test_split.R |only man/gm_geometries.Rd | 6 - src/RcppExports.cpp | 70 ++++++++++--- src/columns.cpp | 21 ++++ src/coordinates.cpp | 4 src/geometries.cpp | 5 src/shapes.cpp | 46 ++++----- src/tests.cpp | 26 ++++- src/utils.cpp | 12 -- 32 files changed, 725 insertions(+), 351 deletions(-)
Title: Nonparametric Methods for Generating High Quality Comparative
Effectiveness Evidence
Description: Implements novel nonparametric approaches to address
biases and confounding when comparing treatments or exposures in
observational studies of outcomes. While designed and appropriate for use
in studies involving medicine and the life sciences, the package can be
used in other situations involving outcomes with multiple confounders.
The package implements a family of methods for non-parametric bias correction
when comparing treatments in observational studies, including survival
analysis settings, where competing risks and/or censoring may be present.
The approach extends to bias-corrected personalized predictions of treatment
outcome differences, and analysis of heterogeneity of treatment effect-sizes
across patient subgroups. For further details, please see:
Lauve NR, Nelson SJ, Young SS, Obenchain RL, Lambert CG. LocalControl:
An R Package for Comparative Safety and Effectiveness Research.
Journal of Statistical Software. 2020. p. 1–32. Available from <doi:10.18637/jss.v096.i04>.
Author: Nicolas R. Lauve [aut] (<https://orcid.org/0000-0002-9348-0319>),
Stuart J. Nelson [aut] (<https://orcid.org/0000-0002-8756-0179>),
S. Stanley Young [aut] (<https://orcid.org/0000-0001-9449-5478>),
Robert L. Obenchain [aut] (<https://orcid.org/0000-0002-8395-1666>),
Melania Pintilie [ctb],
Martin Kutz [ctb],
Christophe G. Lambert [aut, cre]
(<https://orcid.org/0000-0003-1994-2893>)
Maintainer: Christophe G. Lambert <cglambert@unm.edu>
Diff between LocalControl versions 1.1.2.1 dated 2020-04-07 and 1.1.2.2 dated 2020-11-26
DESCRIPTION | 36 ++++++++++++---------- MD5 | 41 +++++++++++++------------- NEWS.md | 6 +++ R/localControl.R | 23 +++++++++++++- README.md | 4 +- build/vignette.rds |binary inst/CITATION |only inst/doc/LocalControl-jss-2018.R | 1 inst/doc/LocalControl-jss-2018.pdf |binary man/LocalControl-deprecated.Rd | 1 man/LocalControl.Rd | 26 ++++++++++++---- man/LocalControlClassic.Rd | 14 ++++++-- man/LocalControlCompetingRisksConfidence.Rd | 13 +++++--- man/LocalControlNearestNeighborsConfidence.Rd | 28 ++++++++++++++--- man/SPSloess.Rd | 13 ++++++-- man/UPSLTDdist.Rd | 9 +++-- man/UPSaltdd.Rd | 14 +++++++- man/cardSim.Rd | 6 ++- man/framingham.Rd | 6 ++- man/lindner.Rd | 6 ++- man/plot.LocalControlCR.Rd | 33 +++++++++++++++----- man/plot.LocalControlCS.Rd | 27 ++++++++++++----- 22 files changed, 218 insertions(+), 89 deletions(-)
Title: Utilities for Japanese Mesh Code
Description: Helpful functions for using mesh code (80km to 125m) data in Japan. Visualize mesh code using 'ggplot2' and 'leaflet', etc.
Author: Shinya Uryu [aut, cre] (<https://orcid.org/0000-0002-0493-6186>)
Maintainer: Shinya Uryu <suika1127@gmail.com>
Diff between jpmesh versions 1.2.1 dated 2020-05-06 and 2.0.0 dated 2020-11-26
DESCRIPTION | 15 MD5 | 124 NAMESPACE | 11 NEWS.md | 8 R/01_imports.R |only R/administration_mesh.R | 23 R/coords_to_mesh.R | 35 R/export_mesh.R | 75 R/find_neighbor_mesh.R | 119 R/fine_separate.R | 113 R/is_mesh.R | 72 R/mesh_convert.R | 191 - R/mesh_to_coords.R | 49 R/meshcode.R |only R/rmesh.R | 19 R/sysdata.rda |binary R/util.R | 235 + build/vignette.rds |binary data/jpnrect.rda |binary data/sf_jpmesh.rda |binary inst/doc/usage.Rmd | 2 inst/doc/usage.html | 296 - man/administration_mesh.Rd | 8 man/coarse_gather.Rd | 4 man/converter.Rd | 7 man/coords_to_mesh.Rd | 3 man/figures/README-jpn_simple_map-1.png |binary man/figures/README-jpn_simple_map_sf-1.png |binary man/fine_separate.Rd | 12 man/mesh_size.Rd | 7 man/mesh_to_coords.Rd | 1 man/meshcode.Rd |only man/meshcode_set.Rd | 8 man/neighbor_mesh.Rd | 2 man/rmesh.Rd | 3 tests/figs/administration-mesh/administration-10kmmesh-pref33-34.svg | 421 +- tests/figs/administration-mesh/administration-10kmmesh-pref35.svg | 229 - tests/figs/administration-mesh/administration-1kmmesh-city08220-08221.svg | 935 ++--- tests/figs/administration-mesh/administration-1kmmesh-city08220.svg | 675 ++-- tests/figs/administration-mesh/administration-1kmmesh-city35201.svg | 1623 ++++------ tests/figs/administration-mesh/administration-80kmmesh-pref08.svg | 23 tests/figs/data/japan-rectangle.svg | 94 tests/figs/deps.txt | 2 tests/figs/find/neighbor-mesh-10km-6meshes.svg | 25 tests/figs/find/neighbor-mesh-1km-self-contains-false.svg | 29 tests/figs/find/neighbor-mesh-1km-self-contains-true.svg | 31 tests/figs/find/neighbor-mesh-80km-7meshes.svg | 27 tests/figs/find/neighbor-mesh-80km.svg | 31 tests/figs/separate-more-fine-mesh-order/fine-separate-10km.svg | 213 - tests/figs/separate-more-fine-mesh-order/fine-separate-1km.svg | 21 tests/figs/separate-more-fine-mesh-order/fine-separate-80km.svg | 141 tests/testthat/test-administration_mesh.R | 30 tests/testthat/test-converter.R | 59 tests/testthat/test-coords_to_meshcode.R | 121 tests/testthat/test-data.R | 11 tests/testthat/test-export_mesh.R | 13 tests/testthat/test-find.R | 88 tests/testthat/test-fine_separate.R | 68 tests/testthat/test-internal.R | 65 tests/testthat/test-mesh_to_coords.R | 45 tests/testthat/test-meshcode.R |only tests/testthat/test-neighborhood.R | 34 tests/testthat/test-rmesh.R | 9 tests/testthat/test-utities.R | 42 vignettes/usage.Rmd | 2 65 files changed, 3378 insertions(+), 3171 deletions(-)
Title: FROC Analysis by Bayesian Approaches
Description: Execute BayesianFROC::fit_GUI_Shiny() (or fit_GUI_Shiny_MRMC()) for a graphical user interface via Shiny. Provides new methods for the so-called Free-response Receiver Operating Characteristic (FROC) analysis. The ultimate aim of FROC analysis is to compare observer performances, which means comparing characteristics, such as area under the curve (AUC) or figure of merit (FOM). In this package, we only use the notion of AUC for modality comparison, where by "modality", we mean imaging methods such as Magnetic Resonance Imaging (MRI), Computed Tomography (CT), Positron Emission Tomography (PET), ..., etc. So there is a problem that which imaging method is better to detect lesions from shadows in radiographs. To solve modality comparison issues, this package provides new methods using hierarchical Bayesian models proposed by the author of this package. Using this package, one can obtain at least one conclusion that which imaging methods are better for finding lesions in radiographs with the case of your data. Fitting FROC statistical models is sometimes not so good, it can easily confirm by drawing FROC curves and comparing these curves and the points constructed by False Positive fractions (FPFs) and True Positive Fractions (TPFs), we can validate the goodness of fit intuitively. Such validation is also implemented by the Chi square goodness of fit statistics in the Bayesian context which means that the parameter is not deterministic, thus by integrating it with the posterior predictive measure, we get a desired value. To compare modalities (imaging methods: MRI, CT, PET, ... , etc), we evaluate AUCs for each modality. FROC is developed by Dev Chakraborty, his FROC model in his 1989 paper relies on the maximal likelihood methodology. The author modified and provided the alternative Bayesian FROC model. Strictly speaking, his model does not coincide with models in this package. In FROC context, we means by multiple reader and multiple case (MRMC) the case of the number of reader or modality is two or more. The MRMC data is available for functions of this package. I hope that medical researchers use not only the frequentist method but also alternative Bayesian methods. In medical research, many problems are considered under only frequentist methods, such as the notion of p-values. But p-value is sometimes misunderstood. Bayesian methods provide very simple, direct, intuitive answer for research questions. Combining frequentist methods with Bayesian methods, we can obtain more reliable answer for research questions. Please execute the following R scripts from the R (R studio) console, demo(demo_MRMC, package = "BayesianFROC"); demo(demo_srsc, package = "BayesianFROC"); demo(demo_stan, package = "BayesianFROC"); demo(demo_drawcurves_srsc, package = "BayesianFROC"); demo_Bayesian_FROC(); demo_Bayesian_FROC_without_pause(). References: Dev Chakraborty (1989) <doi:10.1118/1.596358> Maximum likelihood analysis of free - response receiver operating characteristic (FROC) data. Pre-print: Issei Tsunoda; Bayesian Models for free-response receiver operating characteristic analysis.
Author: Issei Tsunoda [aut, cre]
Maintainer: Issei Tsunoda <tsunoda.issei1111@gmail.com>
Diff between BayesianFROC versions 0.3.1 dated 2020-09-14 and 0.4.0 dated 2020-11-26
DESCRIPTION | 55 MD5 | 185 - NAMESPACE | 10 NEWS.md | 145 + R/BayesianFROC.R | 93 R/Color_Message.R |only R/CoronaVirus_Disease_2019.R | 4 R/DrawCurves.R | 22 R/StartupMessage.R | 44 R/check_cohomology.R |only R/check_rhat.R | 2 R/chi_square_goodness_of_fit.R | 60 R/convertFromJafroc.R | 8 R/create_dataset.R | 4 R/document_dataset_MRMC.R | 4 R/document_dataset_srsc.R | 264 ++ R/draw_latent_distribution.R | 2 R/error_plot.R |only R/extract_EAP_by_array.R | 25 R/fffaaabbb.R | 31 R/file_remove.R | 4 R/fit_Bayesian_FROC.R | 166 + R/fit_GUI.R | 2 R/fit_GUI_Shiny.R | 1371 +++++++---- R/fut_GUI_MRMC_shiny.R | 37 R/h_moll.R |only R/is_logical_0.R |only R/metadata.R | 10 R/p_value_visualization.R |only R/plot_empirical_ROC_curves.R |only R/ppp.R | 184 + R/ppp_vectorization.R |only R/showGraphicalModel.R | 36 R/stanfitExtended.R | 2 R/tracePlotFROC.R | 2 R/validation_MRMC_Create_dataList_MRMC_Hit_from_rate_etc.R | 9 R/validation_error_srsc.R | 2 README.md | 149 - build/vignette.rds |binary data/data_low_p_value.rda |only data/data_much_low_p_value.rda |only demo/00Index | 2 demo/demo_for_compilation_of_all_models.R | 2 demo/demo_ppp.R | 6 demo/demo_ppp_plot_new.R |only inst/CITATION | 12 inst/doc/Implemented_Models.R | 4 inst/doc/Implemented_Models.Rmd | 134 - inst/doc/Implemented_Models.html | 314 +- inst/doc/References.Rnw | 5 inst/doc/References.pdf |binary inst/extdata/Model_MRMC_Multinomial.stan |only inst/extdata/Model_srscVer2.stan | 12 inst/extdata/Model_srsc_multinomial.stan | 205 + man/BayesianFROC.Rd | 90 man/Confirm_hit_rates_are_correctly_made_in_case_of_MRMC.Rd | 9 man/CoronaVirus_Disease_2019.Rd | 2 man/CoronaVirus_Disease_2019_prevalence.Rd | 2 man/Credible_Interval_for_curve.Rd | 4 man/Empirical_FROC_via_ggplot.Rd | 4 man/ROC_data_creator.Rd |only man/array_of_hit_and_false_alarms_from_vector.Rd | 8 man/check_hit_is_less_than_NL.Rd | 4 man/check_rhat.Rd | 2 man/chi_square_at_replicated_data_and_MCMC_samples_MRMC.Rd | 2 man/chi_square_goodness_of_fit.Rd | 2 man/chi_square_goodness_of_fit_from_input_all_param.Rd | 55 man/chi_square_goodness_of_fit_from_input_all_param_MRMC.Rd | 4 man/color_message.Rd |only man/convertFromJafroc.Rd | 8 man/create_dataset.Rd | 4 man/data.nonconverge.srsc.Rd | 3 man/data_low_p_value.Rd |only man/data_much_low_p_value.Rd |only man/ddd.Rd | 2 man/dddddd.Rd | 2 man/draw.CFP.CTP.from.dataList.Rd | 4 man/draw_latent_signal_distribution.Rd | 2 man/extract_EAP_CI.Rd | 25 man/fffaaabbb.Rd | 11 man/fit_Bayesian_FROC.Rd | 104 man/fit_GUI_Shiny.Rd | 59 man/fit_MRMC.Rd | 4 man/fit_MRMC_versionTWO.Rd | 4 man/fit_a_model_to.Rd | 10 man/ggplotFROC.EAP.Rd | 4 man/ggplotFROC.Rd | 4 man/give_name_srsc_data.Rd | 4 man/grapes-greater-than-greater-than-grapes.Rd | 4 man/initial_values_specification_for_stan_in_case_of_MRMC.Rd | 4 man/is_length_zero.Rd |only man/is_logical_0.Rd |only man/is_stanfitExtended.Rd |only man/metadata_to_fit_MRMC.Rd | 8 man/p_value_visualization.Rd |only man/plot_FPF_and_TPF_from_a_dataset.Rd | 4 man/plot_dataset_of_ppp.Rd |only man/plot_dataset_of_ppp_MRMC.Rd |only man/plot_empirical_ROC_curves.Rd |only man/ppp_srsc.Rd | 86 man/showGM.Rd | 7 man/trace_Plot.Rd | 2 man/validation.dataset_srsc.Rd | 2 vignettes/Implemented_Models.Rmd | 134 - vignettes/References.Rnw | 5 105 files changed, 3148 insertions(+), 1178 deletions(-)
Title: Tables of Descriptive Statistics in HTML
Description: Create HTML tables of descriptive statistics, as one would expect
to see as the first table (i.e. "Table 1") in a medical/epidemiological journal
article.
Author: Benjamin Rich [aut, cre, cph]
Maintainer: Benjamin Rich <mail@benjaminrich.net>
Diff between table1 versions 1.2 dated 2020-03-23 and 1.2.1 dated 2020-11-26
DESCRIPTION | 13 - MD5 | 20 +- NEWS.md | 6 R/table1.R | 47 ++++-- build/vignette.rds |binary inst/doc/table1-examples.R | 13 - inst/doc/table1-examples.Rmd | 15 -- inst/doc/table1-examples.html | 146 +++++++++----------- man/signif_pad.Rd | 143 +++++++++---------- man/table1.Rd | 301 +++++++++++++++++++++--------------------- vignettes/table1-examples.Rmd | 15 -- 11 files changed, 356 insertions(+), 363 deletions(-)
Title: An Implementation of Matrix Mathematics
Description: An implementation of matrix mathematics wherein operations are performed "by name."
Author: Matthew Heun [aut, cre] (<https://orcid.org/0000-0002-7438-214X>)
Maintainer: Matthew Heun <matthew.heun@me.com>
Diff between matsbyname versions 0.4.15 dated 2020-05-29 and 0.4.16 dated 2020-11-26
DESCRIPTION | 10 MD5 | 38 - NEWS.md | 21 + R/Unary.R | 89 +++- R/Utilities.R | 8 R/notation.R | 2 build/vignette.rds |binary inst/CITATION | 4 inst/doc/about-vector-arguments.html | 484 +++++++++++++----------- inst/doc/applybyname-vignette.Rmd | 4 inst/doc/applybyname-vignette.html | 140 +++++-- inst/doc/matsbyname.Rmd | 20 - inst/doc/matsbyname.html | 696 +++++++++++++++++++---------------- man/colsums_byname.Rd | 8 man/hatize_byname.Rd | 19 man/rowsums_byname.Rd | 8 tests/testthat/test_Unary.R | 77 +++ tests/testthat/test_Utilities.R | 1 vignettes/applybyname-vignette.Rmd | 4 vignettes/matsbyname.Rmd | 20 - 20 files changed, 1001 insertions(+), 652 deletions(-)
Title: R Interface to Apache Spark
Description: R interface to Apache Spark, a fast and general engine for big data
processing, see <http://spark.apache.org>. This package supports connecting to
local and remote Apache Spark clusters, provides a 'dplyr' compatible back-end,
and provides an interface to Spark's built-in machine learning algorithms.
Author: Javier Luraschi [aut],
Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>),
Kevin Ushey [aut],
JJ Allaire [aut],
Samuel Macedo [ctb],
Hossein Falaki [aut],
Lu Wang [aut],
Andy Zhang [aut],
Yitao Li [aut, cre] (<https://orcid.org/0000-0002-1261-905X>),
Jozef Hajnala [ctb],
Maciej Szymkiewicz [ctb] (<https://orcid.org/0000-0003-1469-9396>),
Wil Davis [ctb],
RStudio [cph],
The Apache Software Foundation [aut, cph]
Maintainer: Yitao Li <yitao@rstudio.com>
Diff between sparklyr versions 1.4.0 dated 2020-09-16 and 1.5.0 dated 2020-11-25
sparklyr-1.4.0/sparklyr/R/logs |only sparklyr-1.4.0/sparklyr/R/metastore_db |only sparklyr-1.5.0/sparklyr/DESCRIPTION | 52 - sparklyr-1.5.0/sparklyr/MD5 | 321 +----- sparklyr-1.5.0/sparklyr/NAMESPACE | 22 sparklyr-1.5.0/sparklyr/NEWS.md | 95 + sparklyr-1.5.0/sparklyr/R/arrow_data.R | 56 - sparklyr-1.5.0/sparklyr/R/browse_url.R |only sparklyr-1.5.0/sparklyr/R/config_settings.R | 1 sparklyr-1.5.0/sparklyr/R/connection_progress.R | 5 sparklyr-1.5.0/sparklyr/R/connection_viewer.R | 6 sparklyr-1.5.0/sparklyr/R/core_deserialize.R | 4 sparklyr-1.5.0/sparklyr/R/core_worker_config.R | 4 sparklyr-1.5.0/sparklyr/R/data_copy.R | 191 +-- sparklyr-1.5.0/sparklyr/R/dbi_spark_connection.R | 14 sparklyr-1.5.0/sparklyr/R/do_spark.R | 91 + sparklyr-1.5.0/sparklyr/R/dplyr_hof.R | 11 sparklyr-1.5.0/sparklyr/R/dplyr_spark_connection.R | 148 ++ sparklyr-1.5.0/sparklyr/R/dplyr_sql.R | 193 +++ sparklyr-1.5.0/sparklyr/R/install_spark_versions.R | 2 sparklyr-1.5.0/sparklyr/R/livy_connection.R | 128 -- sparklyr-1.5.0/sparklyr/R/reexports.R | 11 sparklyr-1.5.0/sparklyr/R/sdf_interface.R | 210 +++- sparklyr-1.5.0/sparklyr/R/sdf_sequence.R | 4 sparklyr-1.5.0/sparklyr/R/sdf_unnest_longer.R |only sparklyr-1.5.0/sparklyr/R/sdf_unnest_wider.R |only sparklyr-1.5.0/sparklyr/R/shell_connection.R | 26 sparklyr-1.5.0/sparklyr/R/spark_apply.R | 22 sparklyr-1.5.0/sparklyr/R/spark_apply_bundle.R | 5 sparklyr-1.5.0/sparklyr/R/spark_connection.R | 58 - sparklyr-1.5.0/sparklyr/R/stratified_sample.R |only sparklyr-1.5.0/sparklyr/R/stream_data.R | 4 sparklyr-1.5.0/sparklyr/R/stream_operations.R | 137 ++ sparklyr-1.5.0/sparklyr/R/tables_spark.R | 2 sparklyr-1.5.0/sparklyr/R/tidyr_nest.R | 3 sparklyr-1.5.0/sparklyr/R/tidyr_pivot_longer.R | 1 sparklyr-1.5.0/sparklyr/R/tidyr_pivot_wider.R | 4 sparklyr-1.5.0/sparklyr/R/tidyr_unnest.R | 2 sparklyr-1.5.0/sparklyr/R/tidyr_utils.R | 41 sparklyr-1.5.0/sparklyr/R/utils.R | 14 sparklyr-1.5.0/sparklyr/R/worker_apply.R | 47 sparklyr-1.5.0/sparklyr/inst/extdata/versions.json | 42 sparklyr-1.5.0/sparklyr/inst/java/sparklyr-1.5-2.10.jar |binary sparklyr-1.5.0/sparklyr/inst/java/sparklyr-1.6-2.10.jar |binary sparklyr-1.5.0/sparklyr/inst/java/sparklyr-2.0-2.11.jar |binary sparklyr-1.5.0/sparklyr/inst/java/sparklyr-2.3-2.11.jar |binary sparklyr-1.5.0/sparklyr/inst/java/sparklyr-2.4-2.11.jar |binary sparklyr-1.5.0/sparklyr/inst/java/sparklyr-2.4-2.12.jar |binary sparklyr-1.5.0/sparklyr/inst/java/sparklyr-3.0-2.12.jar |binary sparklyr-1.5.0/sparklyr/inst/java/sparklyr-master-2.12.jar |binary sparklyr-1.5.0/sparklyr/java/embedded_sources.R | 55 - sparklyr-1.5.0/sparklyr/java/spark-1.5.2/collectors.scala | 40 sparklyr-1.5.0/sparklyr/java/spark-1.5.2/handler.scala | 16 sparklyr-1.5.0/sparklyr/java/spark-1.5.2/partitionutils.scala |only sparklyr-1.5.0/sparklyr/java/spark-1.5.2/rutils.scala |only sparklyr-1.5.0/sparklyr/java/spark-1.5.2/samplingutils.scala | 67 - sparklyr-1.5.0/sparklyr/java/spark-1.5.2/serializer.scala | 518 +++++----- sparklyr-1.5.0/sparklyr/java/spark-1.5.2/sparksqlutils.scala |only sparklyr-1.5.0/sparklyr/java/spark-1.5.2/stream.scala | 28 sparklyr-1.5.0/sparklyr/java/spark-1.5.2/strsplit.scala |only sparklyr-1.5.0/sparklyr/java/spark-1.5.2/udfutils.scala | 9 sparklyr-1.5.0/sparklyr/java/spark-1.5.2/utils.scala | 147 ++ sparklyr-1.5.0/sparklyr/java/spark-1.6.0/cumprod.scala |only sparklyr-1.5.0/sparklyr/java/spark-1.6.0/udfutils.scala |only sparklyr-1.5.0/sparklyr/java/spark-2.0.0/partitionutils.scala |only sparklyr-1.5.0/sparklyr/java/spark-2.0.0/sparksqlutils.scala |only sparklyr-1.5.0/sparklyr/java/spark-2.0.0/streamutils.scala |only sparklyr-1.5.0/sparklyr/java/spark-3.0.0/stratifiedsamplingutils.scala |only sparklyr-1.5.0/sparklyr/man/arrow_enabled_object.Rd |only sparklyr-1.5.0/sparklyr/man/distinct.Rd |only sparklyr-1.5.0/sparklyr/man/grapes-greater-than-grapes.Rd | 4 sparklyr-1.5.0/sparklyr/man/join.tbl_spark.Rd | 18 sparklyr-1.5.0/sparklyr/man/pipe.Rd | 3 sparklyr-1.5.0/sparklyr/man/registerDoSpark.Rd | 11 sparklyr-1.5.0/sparklyr/man/sdf_copy_to.Rd | 3 sparklyr-1.5.0/sparklyr/man/sdf_expand_grid.Rd |only sparklyr-1.5.0/sparklyr/man/sdf_partition_sizes.Rd |only sparklyr-1.5.0/sparklyr/man/sdf_quantile.Rd | 3 sparklyr-1.5.0/sparklyr/man/sdf_seq.Rd | 4 sparklyr-1.5.0/sparklyr/man/sdf_unnest_longer.Rd |only sparklyr-1.5.0/sparklyr/man/sdf_unnest_wider.Rd |only sparklyr-1.5.0/sparklyr/man/stream_lag.Rd |only sparklyr-1.5.0/sparklyr/man/stream_read_delta.Rd | 2 sparklyr-1.5.0/sparklyr/man/stream_write_delta.Rd | 2 sparklyr-1.5.0/sparklyr/man/sub-.tbl_spark.Rd |only 85 files changed, 1772 insertions(+), 1135 deletions(-)
Title: A Toolbox for Manipulating Biological Sequences
Description: Classes and functions to work with biological sequences (DNA, RNA and amino acid sequences).
Implements S3 infrastructure to work with biological sequences as described in Keck (2020) <doi:10.1111/2041-210X.13490>.
Provides a collection of functions to perform biological conversion among classes
(transcription, translation) and basic operations on sequences
(detection, selection and replacement based on positions or patterns).
The package also provides functions to import and export sequences from and to other package formats.
Author: Francois Keck [aut, cre, cph] (<https://orcid.org/0000-0002-3323-4167>)
Maintainer: Francois Keck <francois.keck@gmail.com>
Diff between bioseq versions 0.1.1 dated 2020-07-26 and 0.1.2 dated 2020-11-25
DESCRIPTION | 10 - MD5 | 115 ++++++++++---------- NEWS.md | 21 +++ R/def_aa.R | 3 R/def_dna.R | 3 R/def_rna.R | 3 R/gui_wrappers.R | 14 -- R/print_format.R | 3 R/read_write_fasta.R | 14 ++ R/zzz.R |only README.md | 6 + inst/CITATION |only inst/doc/intro-bioseq.html | 64 +++++++++++ inst/doc/ref_database.html | 128 +++++++++++++++++------ man/aa.Rd | 4 man/aliview.Rd | 10 + man/as-tibble-ape.Rd | 12 +- man/as-tibble-bioseq.Rd | 12 +- man/as_AAbin.Rd | 12 +- man/as_DNAbin.Rd | 12 +- man/as_aa.Rd | 12 +- man/as_dna.Rd | 12 +- man/as_rna.Rd | 12 +- man/as_seqinr_alignment.Rd | 12 +- man/bioseq-package.Rd | 6 - man/dna.Rd | 4 man/figures/logo.png |only man/figures/logo.svg |only man/fragilaria.Rd | 4 man/read_fasta.Rd | 3 man/rev_complement.Rd | 6 - man/rna.Rd | 4 man/seaview.Rd | 8 + man/seq-replace.Rd | 25 ++-- man/seq_cluster.Rd | 3 man/seq_combine.Rd | 25 ++-- man/seq_consensus.Rd | 6 - man/seq_count_pattern.Rd | 25 ++-- man/seq_crop_pattern.Rd | 25 ++-- man/seq_crop_position.Rd | 25 ++-- man/seq_detect_pattern.Rd | 25 ++-- man/seq_disambiguate_IUPAC.Rd | 9 + man/seq_extract_pattern.Rd | 25 ++-- man/seq_extract_position.Rd | 25 ++-- man/seq_nchar.Rd | 9 + man/seq_nseq.Rd | 9 + man/seq_remove_pattern.Rd | 25 ++-- man/seq_remove_position.Rd | 25 ++-- man/seq_replace_position.Rd | 25 ++-- man/seq_rev_translate.Rd | 6 - man/seq_spellout.Rd | 9 + man/seq_split_kmer.Rd | 25 ++-- man/seq_split_pattern.Rd | 25 ++-- man/seq_stat_gc.Rd | 9 + man/seq_stat_prop.Rd | 9 + man/seq_translate.Rd | 7 - man/transcription.Rd | 7 - man/write_fasta.Rd | 3 tests/testthat/example_fasta_multi_chevron.fasta |only tests/testthat/test-print-methods.R | 30 ++--- tests/testthat/test-read-write-fasta.R | 25 ++++ 61 files changed, 642 insertions(+), 353 deletions(-)
Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features
like the condition system, and core 'Tidyverse' features like tidy
evaluation.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between rlang versions 0.4.8 dated 2020-10-08 and 0.4.9 dated 2020-11-25
rlang-0.4.8/rlang/man/parse_quo.Rd |only rlang-0.4.8/rlang/tests/testthat/test-exec.R |only rlang-0.4.9/rlang/DESCRIPTION | 8 rlang-0.4.9/rlang/MD5 | 153 ++++++++--------- rlang-0.4.9/rlang/NAMESPACE | 7 rlang-0.4.9/rlang/NEWS.md | 65 +++++++ rlang-0.4.9/rlang/R/arg.R | 2 rlang-0.4.9/rlang/R/attr.R | 48 +++++ rlang-0.4.9/rlang/R/call.R | 2 rlang-0.4.9/rlang/R/cnd-abort.R | 20 +- rlang-0.4.9/rlang/R/cnd-entrace.R | 16 + rlang-0.4.9/rlang/R/cnd-error.R | 13 + rlang-0.4.9/rlang/R/cnd-handlers.R | 2 rlang-0.4.9/rlang/R/cnd-message.R | 2 rlang-0.4.9/rlang/R/cnd-signal.R | 66 ++++--- rlang-0.4.9/rlang/R/cnd.R | 32 +-- rlang-0.4.9/rlang/R/compat-zeallot.R |only rlang-0.4.9/rlang/R/deparse.R | 10 + rlang-0.4.9/rlang/R/dots.R | 3 rlang-0.4.9/rlang/R/env-binding.R | 20 ++ rlang-0.4.9/rlang/R/env-special.R | 14 + rlang-0.4.9/rlang/R/env.R | 31 +++ rlang-0.4.9/rlang/R/eval-tidy.R | 3 rlang-0.4.9/rlang/R/eval.R | 54 +++++- rlang-0.4.9/rlang/R/fn.R | 4 rlang-0.4.9/rlang/R/lifecycle-retired.R | 2 rlang-0.4.9/rlang/R/lifecycle.R | 2 rlang-0.4.9/rlang/R/nse-defuse.R | 47 +++++ rlang-0.4.9/rlang/R/parse.R | 53 +++-- rlang-0.4.9/rlang/R/utils.R | 17 - rlang-0.4.9/rlang/build/rlang.pdf |binary rlang-0.4.9/rlang/man/abort.Rd | 31 ++- rlang-0.4.9/rlang/man/cnd.Rd | 22 -- rlang-0.4.9/rlang/man/cnd_signal.Rd | 19 -- rlang-0.4.9/rlang/man/enquo0.Rd |only rlang-0.4.9/rlang/man/env_bind.Rd | 9 + rlang-0.4.9/rlang/man/env_browse.Rd |only rlang-0.4.9/rlang/man/env_has.Rd | 4 rlang-0.4.9/rlang/man/env_print.Rd | 6 rlang-0.4.9/rlang/man/env_unbind.Rd | 3 rlang-0.4.9/rlang/man/format_error_bullets.Rd | 2 rlang-0.4.9/rlang/man/inject.Rd |only rlang-0.4.9/rlang/man/nse-defuse.Rd | 4 rlang-0.4.9/rlang/man/parse_expr.Rd | 37 +++- rlang-0.4.9/rlang/man/parse_quosure.Rd | 5 rlang-0.4.9/rlang/man/search_envs.Rd | 7 rlang-0.4.9/rlang/man/tidyeval-data.Rd | 3 rlang-0.4.9/rlang/man/zap_srcref.Rd |only rlang-0.4.9/rlang/src/Makevars | 1 rlang-0.4.9/rlang/src/capture.c | 2 rlang-0.4.9/rlang/src/export/exported.c | 30 +++ rlang-0.4.9/rlang/src/export/init.c | 40 +++- rlang-0.4.9/rlang/src/internal.c | 1 rlang-0.4.9/rlang/src/internal/arg.c | 11 - rlang-0.4.9/rlang/src/internal/dots.c | 27 +-- rlang-0.4.9/rlang/src/internal/env-binding.c | 2 rlang-0.4.9/rlang/src/internal/eval-tidy.c | 43 +++- rlang-0.4.9/rlang/src/internal/nse-defuse.c |only rlang-0.4.9/rlang/src/internal/utils.c | 28 +++ rlang-0.4.9/rlang/src/internal/utils.h | 3 rlang-0.4.9/rlang/src/lib/c-utils.h |only rlang-0.4.9/rlang/src/lib/cnd.h | 2 rlang-0.4.9/rlang/src/lib/parse.c | 28 ++- rlang-0.4.9/rlang/src/lib/parse.h | 2 rlang-0.4.9/rlang/src/lib/rlang.c | 2 rlang-0.4.9/rlang/src/lib/rlang.h | 9 + rlang-0.4.9/rlang/src/version.c | 2 rlang-0.4.9/rlang/tests/sink.R | 16 - rlang-0.4.9/rlang/tests/testthat/helper-rlang.R | 15 + rlang-0.4.9/rlang/tests/testthat/test-attr.R | 39 ++++ rlang-0.4.9/rlang/tests/testthat/test-c-api.R | 2 rlang-0.4.9/rlang/tests/testthat/test-cnd-entrace.R | 19 ++ rlang-0.4.9/rlang/tests/testthat/test-cnd-handlers.R | 5 rlang-0.4.9/rlang/tests/testthat/test-cnd-signal.R | 25 ++ rlang-0.4.9/rlang/tests/testthat/test-compat-zeallot.R |only rlang-0.4.9/rlang/tests/testthat/test-deparse.R | 5 rlang-0.4.9/rlang/tests/testthat/test-env.R | 13 + rlang-0.4.9/rlang/tests/testthat/test-eval-tidy.R | 10 - rlang-0.4.9/rlang/tests/testthat/test-eval.R |only rlang-0.4.9/rlang/tests/testthat/test-fn.R | 25 ++ rlang-0.4.9/rlang/tests/testthat/test-nse-defuse.R | 24 ++ rlang-0.4.9/rlang/tests/testthat/test-nse-force.R | 6 rlang-0.4.9/rlang/tests/testthat/test-utils.R | 6 83 files changed, 967 insertions(+), 324 deletions(-)
Title: Create Credit State Migration (Transition) Matrices
Description: Tools to help convert credit risk data at two time points
into traditional credit state migration (aka, "transition") matrices.
At a higher level, 'migrate' is intended to help an analyst understand
how risk moved in their credit portfolio over a time interval.
References to this methodology include:
1. Schuermann, T. (2008) <doi:10.1002/9780470061596.risk0409>.
2. Perederiy, V. (2017) <arXiv:1708.00062>.
Author: Michael Thomas [aut, cre],
Brad Lindblad [ctb]
Maintainer: Michael Thomas <mthomas@ketchbrookanalytics.com>
Diff between migrate versions 0.1.0 dated 2020-11-24 and 0.2.0 dated 2020-11-25
DESCRIPTION | 6 +- MD5 | 19 +++--- NEWS.md | 4 + R/migrate.R | 135 +++++++++++++++++++++++-------------------------- README.md | 37 +++++++++++++ inst/doc/migrate.R | 51 +++++++++--------- inst/doc/migrate.Rmd | 15 ++--- inst/doc/migrate.html | 53 +++++++++++++++---- man/figures/gt_tbl.png |only man/migrate.Rd | 41 +++++--------- vignettes/migrate.Rmd | 15 ++--- 11 files changed, 218 insertions(+), 158 deletions(-)
Title: Identifying Functional Polymorphisms
Description: A suite for identifying causal models using relative concordances and identifying causal polymorphisms in case-control genetic association data, especially with large controls re-sequenced data.
Author: Park L
Maintainer: Leeyoung Park <lypark@yonsei.ac.kr>
Diff between IFP versions 0.2.3 dated 2020-10-26 and 0.2.4 dated 2020-11-25
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- man/iter.mcmc.Rd | 7 +++++-- man/lrt.G.Rd | 7 +++++-- man/lrt.Rd | 3 +++ 5 files changed, 20 insertions(+), 11 deletions(-)
Title: Analysis and Simulation of Plant Disease Progress Curves
Description: Analysis and visualization of plant disease progress curve data. Functions for
fitting two-parameter population dynamics models (exponential, monomolecular, logistic
and Gompertz) to proportion data for single or multiple epidemics using either linear
or no-linear regression. Statistical and visual outputs are provided to aid in model
selection. Synthetic curves can be simulated for any of the models given the parameters.
See Laurence V. Madden, Gareth Hughes, and Frank van den Bosch (2007) <doi:10.1094/9780890545058>
for further information on the methods.
Author: Kaique dos S. Alves [aut, cre]
(<https://orcid.org/0000-0001-9187-0252>),
Emerson M. Del Ponte [aut] (<https://orcid.org/0000-0003-4398-409X>)
Maintainer: Kaique dos S. Alves <kaiquedsalves@gmail.com>
Diff between epifitter versions 0.1.0 dated 2020-10-29 and 0.2.0 dated 2020-11-25
DESCRIPTION | 6 MD5 | 17 - NEWS.md |only R/fit_lin.R | 32 +- R/fit_nlin.R | 4 R/fit_nlin2.R | 14 R/sim_monomolecular.R | 10 README.md | 12 inst/doc/fitting.html | 734 +++++++++++++++++++++++------------------------ inst/doc/simulation.html | 378 +++++++++++------------- 10 files changed, 601 insertions(+), 606 deletions(-)
Title: Prioritizing Cancer Driver Genes Using Genomics Data
Description: Cancer genomes contain large numbers of somatic alterations but few
genes drive tumor development. Identifying cancer driver genes is critical
for precision oncology. Most of current approaches either identify driver
genes based on mutational recurrence or using estimated scores predicting
the functional consequences of mutations. 'driveR' is a tool for
personalized or batch analysis of genomic data for driver gene prioritization
by combining genomic information and prior biological knowledge. As features,
'driveR' uses coding impact metaprediction scores, non-coding impact scores,
somatic copy number alteration scores, hotspot gene/double-hit gene
condition, 'phenolyzer' gene scores and memberships to cancer-related KEGG
pathways. It uses these features to estimate cancer-type-specific
probability for each gene of being a cancer driver using the related task of
a multi-task learning classification model. The method is described in detail
in Ulgen E, Sezerman OU. 2020. driveR: A Novel Method for Prioritizing Cancer
Driver Genes Using Somatic Genomics Data. bioRxiv
<doi:10.1101/2020.11.10.376707>.
Author: Ege Ulgen [aut, cre, cph] (<https://orcid.org/0000-0003-2090-3621>)
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between driveR versions 0.2.0 dated 2020-11-19 and 0.2.1 dated 2020-11-25
DESCRIPTION | 13 ++++------ MD5 | 28 +++++++++++------------ NAMESPACE | 1 NEWS.md | 24 +++++++++++++++---- R/core_functions.R | 4 ++- R/data.R | 5 ++-- R/sysdata.rda |binary README.md | 6 ++++ data/example_cohort_features_table.rda |binary data/example_features_table.rda |binary data/specific_thresholds.rda |binary inst/doc/how_to_use.html | 40 ++++++++++++++++----------------- man/KEGG_cancer_pathways.Rd | 2 - man/MCR_table.Rd | 3 +- tests/testthat/test-core_functions.R | 4 ++- 15 files changed, 78 insertions(+), 52 deletions(-)
Title: Tunes AdaBoost, Elastic Net, Support Vector Machines, and
Gradient Boosting Machines
Description: Contains two functions that are intended to make
tuning supervised learning methods easy. The eztune function uses a
genetic algorithm or Hooke-Jeeves optimizer to find the best
set of tuning parameters. The user can choose the optimizer, the
learning method, and if optimization will be based on accuracy
obtained through validation error, cross validation, or resubstitution.
The function eztune.cv will compute a cross validated error rate. The purpose
of eztune_cv is to provide a cross validated accuracy or MSE when
resubstitution or validation data are used for optimization because
error measures from both approaches can be misleading.
Author: Jill Lundell [aut, cre]
Maintainer: Jill Lundell <jflundell@gmail.com>
Diff between EZtune versions 2.0.0 dated 2019-06-29 and 3.0.0 dated 2020-11-25
EZtune-2.0.0/EZtune/R/misc.R |only EZtune-2.0.0/EZtune/data/datalist |only EZtune-2.0.0/EZtune/inst/doc/EZtune.R |only EZtune-2.0.0/EZtune/inst/doc/EZtune.Rmd |only EZtune-2.0.0/EZtune/inst/doc/EZtune.html |only EZtune-2.0.0/EZtune/vignettes/EZtune.Rmd |only EZtune-3.0.0/EZtune/DESCRIPTION | 14 - EZtune-3.0.0/EZtune/MD5 | 65 ++++--- EZtune-3.0.0/EZtune/NAMESPACE | 12 - EZtune-3.0.0/EZtune/R/ada_bin.R | 64 +++---- EZtune-3.0.0/EZtune/R/ada_bin_ga.R | 66 +++---- EZtune-3.0.0/EZtune/R/cv_tests.R | 234 +++++++++++++++----------- EZtune-3.0.0/EZtune/R/dummy.R |only EZtune-3.0.0/EZtune/R/en_bin.R |only EZtune-3.0.0/EZtune/R/en_bin_ga.R |only EZtune-3.0.0/EZtune/R/en_reg.R |only EZtune-3.0.0/EZtune/R/en_reg_ga.R |only EZtune-3.0.0/EZtune/R/eztune.R | 98 ++++++---- EZtune-3.0.0/EZtune/R/eztune_cv.R | 31 ++- EZtune-3.0.0/EZtune/R/findn.R |only EZtune-3.0.0/EZtune/R/gbm_bin.R | 79 ++++---- EZtune-3.0.0/EZtune/R/gbm_bin_ga.R | 82 ++++----- EZtune-3.0.0/EZtune/R/gbm_reg.R | 64 +++---- EZtune-3.0.0/EZtune/R/gbm_reg_ga.R | 63 +++---- EZtune-3.0.0/EZtune/R/loss.R |only EZtune-3.0.0/EZtune/R/svm_bin.R | 75 ++++---- EZtune-3.0.0/EZtune/R/svm_bin_ga.R | 76 +++++--- EZtune-3.0.0/EZtune/R/svm_reg.R | 67 ++++--- EZtune-3.0.0/EZtune/R/svm_reg_ga.R | 66 ++++--- EZtune-3.0.0/EZtune/README.md |only EZtune-3.0.0/EZtune/build/vignette.rds |binary EZtune-3.0.0/EZtune/inst/CITATION | 28 +-- EZtune-3.0.0/EZtune/inst/doc/my-vignette.R |only EZtune-3.0.0/EZtune/inst/doc/my-vignette.Rmd |only EZtune-3.0.0/EZtune/inst/doc/my-vignette.html |only EZtune-3.0.0/EZtune/man/eztune.Rd | 82 +++++---- EZtune-3.0.0/EZtune/man/eztune_cv.Rd | 109 ++++++------ EZtune-3.0.0/EZtune/man/lichen.Rd | 184 ++++++++++---------- EZtune-3.0.0/EZtune/man/lichenTest.Rd | 160 +++++++++-------- EZtune-3.0.0/EZtune/man/mullein.Rd | 160 +++++++++-------- EZtune-3.0.0/EZtune/man/mulleinTest.Rd | 148 ++++++++-------- EZtune-3.0.0/EZtune/vignettes/eztune.bib |only EZtune-3.0.0/EZtune/vignettes/my-vignette.Rmd |only 43 files changed, 1090 insertions(+), 937 deletions(-)
Title: Package for Reading Binary Files
Description: Functions and analytics for GENEA-compatible accelerometer data into R objects.
See topic 'GENEAread' for an introduction to the package.
See <https://www.activinsights.com/products/geneactiv/> for more details on the GENEActiv device.
Author: Zhou Fang [aut],
Joss Langford [aut],
Charles Sweetland [aut, cre]
Maintainer: Charles Sweetland <charles@sweetland-solutions.co.uk>
Diff between GENEAread versions 2.0.8 dated 2019-10-30 and 2.0.9 dated 2020-11-25
DESCRIPTION | 10 MD5 | 34 - R/GRtime.r | 4 R/Recalibrate.R | 96 ++-- R/get.intervals.r | 10 R/header.info.R | 217 ++++----- R/read.bin.R | 1025 +++++++++++++++++++++++---------------------- R/stftmod.R | 2 man/AccData.Rd | 4 man/GENEActiv.calibrate.Rd | 12 man/GENEAread-package.Rd | 23 - man/GRtime.Rd | 11 man/epoch.Rd | 6 man/get.intervals.Rd | 2 man/plot.stft.Rd | 23 - man/recalibrate.Rd | 13 man/seq.log.Rd | 3 man/stftcalc.Rd | 17 18 files changed, 812 insertions(+), 700 deletions(-)
Title: Big Data Preprocessing Architecture
Description: Provide a tool to easily build customized data flows to pre-process large volumes
of information from different sources. To this end, 'bdpar' allows to (i) easily use and
create new functionalities and (ii) develop new data source extractors according to the
user needs. Additionally, the package provides by default a predefined data flow
to extract and pre-process the most relevant information (tokens, dates, ... ) from some textual
sources (SMS, Email, tweets, YouTube comments).
Author: Miguel Ferreiro-Díaz [aut, cre],
David Ruano-Ordás [aut, ctr],
Tomás R. Cotos-Yañez [aut, ctr],
University of Vigo [cph]
Maintainer: Miguel Ferreiro-Díaz <miguel.ferreiro.diaz@gmail.com>
Diff between bdpar versions 2.0.0 dated 2020-02-20 and 3.0.0 dated 2020-11-25
DESCRIPTION | 31 MD5 | 360 +- NAMESPACE | 12 NEWS.md | 19 R/AbbreviationPipe.R | 428 +-- R/Bdpar.R | 447 +++ R/BdparOptions.R | 274 ++ R/Connections.R | 269 -- R/ContractionPipe.R | 435 +-- R/DefaultPipeline.R | 127 - R/DynamicPipeline.R | 307 +- R/ExtractorEml.R | 240 - R/ExtractorFactory.R | 312 +- R/ExtractorSms.R | 111 R/ExtractorTwtid.R | 270 +- R/ExtractorYtbid.R | 291 +- R/File2Pipe.R | 127 - R/FindEmojiPipe.R | 271 -- R/FindEmoticonPipe.R | 258 -- R/FindHashtagPipe.R | 257 -- R/FindUrlPipe.R | 457 +-- R/FindUserNamePipe.R | 259 -- R/GenericPipe.R | 335 +- R/GenericPipeline.R | 93 R/GuessDatePipe.R | 111 R/GuessLanguagePipe.R | 218 - R/Instance.R | 709 +---- R/InterjectionPipe.R | 411 +-- R/MeasureLengthPipe.R | 200 - R/ResourceHandler.R | 147 - R/SlangPipe.R | 427 +-- R/StopWordPipe.R | 424 +-- R/StoreFileExtPipe.R | 163 - R/TargetAssigningPipe.R | 279 -- R/TeeCSVPipe.R | 192 - R/ToLowerCasePipe.R | 150 - R/bdpar.Options.R | 111 R/bdpar.log.R |only R/eml.R | 16 R/operator-pipe.R | 252 +- R/runPipeline.R | 93 R/wrapper.R |only R/zzz.R | 2 build/vignette.rds |binary exec/parse.py | 6 inst/doc/bdpar.R | 29 inst/doc/bdpar.Rmd | 105 inst/doc/bdpar.html | 473 ++- inst/doc/bdparExample.R | 5 inst/doc/bdparExample.Rmd | 11 inst/doc/bdparExample.html | 120 inst/doc/bdparExampleImage.R |only inst/doc/bdparExampleImage.Rmd |only inst/doc/bdparExampleImage.html |only inst/example/testFilesEml/_ham_/00001.1a31cc283af0060967a233d26548a6ce.eml | 3 inst/example/testFilesEml/_ham_/00001.7c53336b37003a9286aba55d2945844c.eml | 3 inst/example/testFilesEml/_ham_/00002.9c4069e25e1ef370c078db7ee85ff9ac.eml | 5 inst/example/testFilesEml/_ham_/00002.ca96f74042d05c1a1d29ca30467cfcd5.eml | 4 inst/example/testFilesEml/_ham_/00003.268fd170a3fc73bee2739d8204856a53.eml | 2 inst/example/testFilesEml/_ham_/00003.860e3c3cee1b42ead714c5c874fe25f7.eml | 5 inst/example/testFilesEml/_ham_/00004.864220c5b6930b209cc287c361c99af1.eml | 2 inst/example/testFilesEml/_ham_/00005.34bcaad58ad5f598f5d6af8cfa0c0465.eml | 7 inst/example/testFilesEml/_ham_/00005.bf27cdeaf0b8c4647ecd61b1d09da613.eml | 5 inst/example/testFilesEml/_ham_/00006.253ea2f9a9cc36fa0b1129b04b806608.eml | 5 inst/example/testFilesEml/_ham_/00008.5891548d921601906337dcf1ed8543cb.eml | 5 inst/example/testFilesEml/_ham_/01391.00e6f3a6dc816f22335f1b0fd6098eda.eml | 4 inst/example/testFilesEml/_ham_/01392.6a9e94b131381aa631022fc1b6c9bdab.eml | 4 inst/example/testFilesEml/_ham_/01394.b4dd1cece01b908f040e33493643c4a4.eml | 5 inst/example/testFilesEml/_ham_/01395.65a2be0a7f93369c253c4bac543fdeb8.eml | 4 inst/example/testFilesEml/_ham_/01399.ca6b00b7b341bbde9a9ea3dd6a7bf896.eml | 4 inst/example/testFilesEml/_ham_/01400.f897f0931e461e7b2e964d28e927c35e.eml | 3 inst/example/testFilesTsms/_ham_/0.tsms | 2 inst/example/testFilesTsms/_ham_/10.tsms | 2 inst/example/testFilesTsms/_ham_/14.tsms | 2 inst/example/testFilesTsms/_ham_/16.tsms | 2 inst/example/testFilesTsms/_ham_/20.tsms | 2 inst/example/testFilesTsms/_ham_/23.tsms | 2 inst/example/testFilesTsms/_ham_/27.tsms | 2 inst/example/testFilesTsms/_ham_/4.tsms | 2 man/AbbreviationPipe.Rd | 318 +- man/Bdpar.Rd | 157 - man/Connections.Rd | 167 - man/ContractionPipe.Rd | 318 +- man/DefaultPipeline.Rd | 133 - man/DynamicPipeline.Rd | 226 + man/ExtractorEml.Rd | 241 + man/ExtractorFactory.Rd | 249 +- man/ExtractorSms.Rd | 141 - man/ExtractorTwtid.Rd | 229 + man/ExtractorYtbid.Rd | 226 + man/File2Pipe.Rd | 148 - man/FindEmojiPipe.Rd | 230 + man/FindEmoticonPipe.Rd | 227 + man/FindHashtagPipe.Rd | 227 + man/FindUrlPipe.Rd | 362 +- man/FindUserNamePipe.Rd | 229 + man/GenericPipe.Rd | 268 +- man/GenericPipeline.Rd | 112 man/GuessDatePipe.Rd | 151 - man/GuessLanguagePipe.Rd | 184 - man/Instance.Rd | 571 ++-- man/InterjectionPipe.Rd | 304 +- man/MeasureLengthPipe.Rd | 185 - man/ResourceHandler.Rd | 140 - man/SlangPipe.Rd | 310 +- man/StopWordPipe.Rd | 304 +- man/StoreFileExtPipe.Rd | 169 - man/TargetAssigningPipe.Rd | 246 + man/TeeCSVPipe.Rd | 177 - man/ToLowerCasePipe.Rd | 166 - man/bdpar.Options.Rd | 116 man/bdpar.log.Rd |only man/bdparData.Rd | 6 man/operator-pipe.Rd | 16 man/runPipeline.Rd | 31 tests/testthat/testFiles/testAbbreviationPipe/testFile.tsms | 2 tests/testthat/testFiles/testBdpar/tsms-1fileInvalid |only tests/testthat/testFiles/testBdpar/tsms/_ham_/30.tsms | 2 tests/testthat/testFiles/testBdpar/tsms/_spam_/1022.tsms | 2 tests/testthat/testFiles/testBdpar/tsms5Files |only tests/testthat/testFiles/testBdparOptions |only tests/testthat/testFiles/testContractionPipe/testFile.tsms | 2 tests/testthat/testFiles/testDefaultPipeline/files/_ham_/testFile.tsms | 2 tests/testthat/testFiles/testDefaultPipeline/testFile.tsms | 2 tests/testthat/testFiles/testDynamicPipeline/files/_ham_/testFile.tsms | 2 tests/testthat/testFiles/testDynamicPipeline/testFile.tsms | 2 tests/testthat/testFiles/testFindEmojiPipe/testFile.tsms | 2 tests/testthat/testFiles/testFindEmoticonPipe/testFile.tsms | 2 tests/testthat/testFiles/testFindHashtagPipe/testFile.tsms | 2 tests/testthat/testFiles/testFindUrlPipe/testFile.tsms | 2 tests/testthat/testFiles/testFindUserNamePipe/testFile.tsms | 2 tests/testthat/testFiles/testGuessDatePipe/testFile.tsms | 2 tests/testthat/testFiles/testGuessLanguagePipe/testFile.tsms | 2 tests/testthat/testFiles/testInstanceFactory/example.twtid | 2 tests/testthat/testFiles/testInstanceFactory/example.ytbid | 2 tests/testthat/testFiles/testInterjectionPipe/testFile.tsms | 2 tests/testthat/testFiles/testMeasureLengthPipe/testFile.tsms | 2 tests/testthat/testFiles/testOperator-pipe |only tests/testthat/testFiles/testRunPipeline/tsms/_ham_/30.tsms | 2 tests/testthat/testFiles/testRunPipeline/tsms/_spam_/1022.tsms | 2 tests/testthat/testFiles/testSlangPipe/testFile.tsms | 2 tests/testthat/testFiles/testStopWordPipe/testFile.tsms | 2 tests/testthat/testFiles/testStoreFileExtPipe/testFile.tsms | 2 tests/testthat/testFiles/testTargetAssigningPipe/files/_ham_/testFile.tsms | 2 tests/testthat/testFiles/testTargetAssigningPipe/testFile.tsms | 2 tests/testthat/testFiles/testTeeCSVPipe/testFile.tsms | 2 tests/testthat/test_AbbreviationPipe.R | 308 +- tests/testthat/test_Bdpar.R | 1242 +++++++++- tests/testthat/test_BdparOptions.R | 282 ++ tests/testthat/test_Connections.R | 77 tests/testthat/test_ContractionPipe.R | 311 +- tests/testthat/test_DefaultPipeline.R | 95 tests/testthat/test_DynamicPipeline.R | 212 + tests/testthat/test_ExtractorEml.R | 120 tests/testthat/test_ExtractorFactory.R | 293 ++ tests/testthat/test_ExtractorSms.R | 88 tests/testthat/test_ExtractorTwtid.R | 12 tests/testthat/test_ExtractorYtbid.R | 12 tests/testthat/test_File2Pipe.R | 83 tests/testthat/test_FindEmojiPipe.R | 185 + tests/testthat/test_FindEmoticonPipe.R | 159 + tests/testthat/test_FindHashtagPipe.R | 159 + tests/testthat/test_FindUrlPipe.R | 305 ++ tests/testthat/test_FindUserNamePipe.R | 159 + tests/testthat/test_GenericPipeline.R | 53 tests/testthat/test_GuessDatePipe.R | 69 tests/testthat/test_GuessLanguagePipe.R | 118 tests/testthat/test_Instance.R | 455 +++ tests/testthat/test_InterjectionPipe.R | 327 +- tests/testthat/test_MeasureLengthPipe.R | 115 tests/testthat/test_Operator-pipe.R |only tests/testthat/test_PipeGeneric.R | 152 + tests/testthat/test_ResourceHandler.R | 82 tests/testthat/test_SlangPipe.R | 345 +- tests/testthat/test_StopWordPipe.R | 330 +- tests/testthat/test_StoreFileExtPipe.R | 103 tests/testthat/test_TargetAssigningPipe.R | 180 + tests/testthat/test_TeeCSVPipe.R | 163 + tests/testthat/test_ToLowerCasePipe.R | 89 tests/testthat/test_bdpar.log.R |only tests/testthat/test_onLoad.R |only tests/testthat/test_runPipeline.R | 265 +- vignettes/bdpar.Rmd | 105 vignettes/bdparExample.Rmd | 11 vignettes/bdparExampleImage.Rmd |only 185 files changed, 15864 insertions(+), 9268 deletions(-)
Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre],
RStudio [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 0.12.2 dated 2020-11-04 and 0.12.3 dated 2020-11-25
DESCRIPTION | 11 - MD5 | 98 ++++++------ NEWS.md | 39 +++++ R/bioconductor.R | 6 R/bootstrap.R | 59 ++++++- R/cache.R | 80 +++++++++- R/dependencies.R | 7 R/files.R | 2 R/hash.R | 4 R/install.R | 13 - R/libpaths.R | 38 +++- R/load.R | 8 - R/lockfile.R | 8 - R/packages.R | 9 + R/patch.R | 44 +++++ R/project.R | 30 +++ R/restore.R | 20 +- R/retrieve.R | 2 R/roxygen.R | 10 - R/settings.R | 17 ++ R/snapshot.R | 2 R/status.R | 18 +- R/testthat-reporter.R | 5 build/vignette.rds |binary inst/doc/ci.html | 237 ------------------------------ inst/doc/collaborating.html | 237 ------------------------------ inst/doc/docker.Rmd | 28 +++ inst/doc/docker.html | 261 +++------------------------------- inst/doc/faq.html | 247 +------------------------------- inst/doc/local-sources.html | 239 ------------------------------- inst/doc/lockfile.html | 239 ------------------------------- inst/doc/mran.html | 247 +------------------------------- inst/doc/packages.html | 237 ------------------------------ inst/doc/python.html | 237 ------------------------------ inst/doc/renv.Rmd | 9 - inst/doc/renv.html | 283 +++---------------------------------- inst/resources/activate.R | 70 +++++++-- man/install.Rd | 2 man/restore.Rd | 6 man/settings.Rd | 12 + man/status.Rd | 7 man/update.Rd | 2 tests/testthat/test-bioconductor.R | 16 ++ tests/testthat/test-bootstrap.R | 13 + tests/testthat/test-cache.R | 28 +++ tests/testthat/test-dependencies.R | 21 +- tests/testthat/test-install.R | 10 + tests/testthat/test-settings.R | 11 + vignettes/docker.Rmd | 28 +++ vignettes/renv.Rmd | 9 - 50 files changed, 741 insertions(+), 2525 deletions(-)
Title: CONCOR and Supplemental Functions
Description: Contains the CONCOR (CONvergence of iterated CORrelations)
algorithm and a series of supplemental functions for easy running,
plotting, and blockmodeling. The CONCOR algorithm is used on social network
data to identify network positions based off a definition of structural
equivalence; see Breiger, Boorman, and Arabie (1975)
<doi:10.1016/0022-2496(75)90028-0> and Wasserman and Faust's book Social
Network Analysis: Methods and Applications (1994). This version allows
multiple relationships for the same set of nodes and uses both incoming and
outgoing ties to find positions.
Author: Tyme Suda [aut],
Adrienne Traxler [cre] (<https://orcid.org/0000-0003-2725-0686>),
Carter Butts [ctb] (Author of sna::plot.blockmodel(), adapted for
plot_blk())
Maintainer: Adrienne Traxler <adrienne.traxler@wright.edu>
Diff between concorR versions 0.2.0 dated 2020-06-03 and 0.2.1 dated 2020-11-25
DESCRIPTION | 6 ++-- MD5 | 26 +++++++++--------- NAMESPACE | 26 +++++++++--------- NEWS.md |only R/CONCOR_supplemental_fun.R | 30 ++++++++++++++++++--- README.md | 13 ++++++--- build/partial.rdb |binary inst |only man/concorigraphapply.Rd | 11 +++++++ man/concormakeigraph.Rd | 19 +++++++++---- man/figures/README-example-basic-1.png |binary man/figures/README-example-basic-2.png |binary man/figures/README-krackhardt-reduced-multi-1.png |binary man/figures/README-krackhardt-reduced-single-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary 15 files changed, 89 insertions(+), 42 deletions(-)
Title: Quick Serialization of R Objects
Description: Provides functions for quickly writing and reading any R object to and from disk.
Author: Travers Ching [aut, cre, cph],
Yann Collet [ctb, cph] (Yann Collet is the author of the bundled zstd,
lz4 and xxHash code),
Facebook, Inc. [cph] (Facebook is the copyright holder of the bundled
zstd code),
Reichardt Tino [ctb, cph] (Contributor/copyright holder of zstd bundled
code),
Skibinski Przemyslaw [ctb, cph] (Contributor/copyright holder of zstd
bundled code),
Mori Yuta [ctb, cph] (Contributor/copyright holder of zstd bundled
code),
Romain Francois [ctb, cph] (Derived example/tutorials for ALTREP
structures),
Francesc Alted [ctb, cph] (Shuffling routines derived from Blosc
library),
Bryce Chamberlain [ctb] (qsame, qload function contributor)
Maintainer: Travers Ching <traversc@gmail.com>
Diff between qs versions 0.23.3 dated 2020-10-05 and 0.23.4 dated 2020-11-25
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/qsavem-load.R | 8 ++++---- R/zzz.R | 2 +- build/vignette.rds |binary inst/doc/vignette.html | 2 +- man/qreadm.Rd | 4 ++-- man/qsavem.Rd | 4 ++-- 9 files changed, 25 insertions(+), 22 deletions(-)
Title: False Discovery Exceedance Controlling Multiple Testing
Procedures
Description: Multiple testing procedures for heterogeneous and discrete tests as described in Döhler and Roquain (2019) <arXiv:1912.04607v1>. The main algorithms of the paper are available as continuous, discrete and weighted versions.
Author: Sebastian Döhler [aut],
Florian Junge [aut, cre],
Etienne Roquain [ctb]
Maintainer: Florian Junge <florian.junge@h-da.de>
Diff between FDX versions 1.0.2 dated 2020-09-02 and 1.0.3 dated 2020-11-25
DESCRIPTION | 11 ++++++----- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/weightedGR_fun.R | 2 +- R/weightedLR_fun.R | 2 +- R/weightedPB_fun.R | 2 +- 6 files changed, 18 insertions(+), 13 deletions(-)
Title: Symbolic Representation of Matrix Determinant
Description: Creates a guide for writing the formula for the determinant of a square matrix (a detguide) as a function of the elements of the matrix and writes out that formula, the symbolic representation.
Author: William Fairweather [aut, cre]
Maintainer: William Fairweather <wrf343@flowervalleyconsulting.com>
Diff between SymbolicDeterminants versions 1.0.2 dated 2020-11-09 and 1.2.0 dated 2020-11-25
SymbolicDeterminants-1.0.2/SymbolicDeterminants/R/initialdets.R |only SymbolicDeterminants-1.0.2/SymbolicDeterminants/R/makedetguide.R |only SymbolicDeterminants-1.0.2/SymbolicDeterminants/R/size.predictor.R |only SymbolicDeterminants-1.0.2/SymbolicDeterminants/R/test.in.order.R |only SymbolicDeterminants-1.0.2/SymbolicDeterminants/inst/doc/background.Rmd |only SymbolicDeterminants-1.0.2/SymbolicDeterminants/inst/doc/background.html |only SymbolicDeterminants-1.0.2/SymbolicDeterminants/man/initialdets.Rd |only SymbolicDeterminants-1.0.2/SymbolicDeterminants/vignettes/background.Rmd |only SymbolicDeterminants-1.2.0/SymbolicDeterminants/DESCRIPTION | 18 ++--- SymbolicDeterminants-1.2.0/SymbolicDeterminants/LICENSE |only SymbolicDeterminants-1.2.0/SymbolicDeterminants/MD5 | 35 +++++----- SymbolicDeterminants-1.2.0/SymbolicDeterminants/NAMESPACE | 5 + SymbolicDeterminants-1.2.0/SymbolicDeterminants/NEWS.md | 16 ++++ SymbolicDeterminants-1.2.0/SymbolicDeterminants/R/anewdetguide.R |only SymbolicDeterminants-1.2.0/SymbolicDeterminants/R/confirm.det.R | 19 ++--- SymbolicDeterminants-1.2.0/SymbolicDeterminants/R/detindex.R |only SymbolicDeterminants-1.2.0/SymbolicDeterminants/R/parsedetguide.R | 25 +++---- SymbolicDeterminants-1.2.0/SymbolicDeterminants/R/predictor.R |only SymbolicDeterminants-1.2.0/SymbolicDeterminants/R/retrieve.R |only SymbolicDeterminants-1.2.0/SymbolicDeterminants/README.md |only SymbolicDeterminants-1.2.0/SymbolicDeterminants/build/vignette.rds |binary SymbolicDeterminants-1.2.0/SymbolicDeterminants/inst/doc/Background.Rmd |only SymbolicDeterminants-1.2.0/SymbolicDeterminants/inst/doc/Background.html |only SymbolicDeterminants-1.2.0/SymbolicDeterminants/man/anewdetguide.Rd |only SymbolicDeterminants-1.2.0/SymbolicDeterminants/man/confirm.det.Rd | 11 +-- SymbolicDeterminants-1.2.0/SymbolicDeterminants/man/detindex.Rd |only SymbolicDeterminants-1.2.0/SymbolicDeterminants/man/predictor.Rd |only SymbolicDeterminants-1.2.0/SymbolicDeterminants/man/retrieve.Rd |only SymbolicDeterminants-1.2.0/SymbolicDeterminants/vignettes/Background.Rmd |only 29 files changed, 73 insertions(+), 56 deletions(-)
More information about SymbolicDeterminants at CRAN
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Title: PARAFAC Analysis of EEMs from DOM
Description: This is a user-friendly way to run a parallel factor (PARAFAC) analysis (Harshman, 1971) <doi:10.1121/1.1977523> on excitation emission matrix (EEM) data from dissolved organic matter (DOM) samples (Murphy et al., 2013) <doi:10.1039/c3ay41160e>. The analysis includes profound methods for model validation. Some additional functions allow the calculation of absorbance slope parameters and create beautiful plots.
Author: Matthias Pucher [aut, cre],
Daniel Graeber [aut, ctb],
Stefan Preiner [ctb],
Renata Pinto [ctb]
Maintainer: Matthias Pucher <matthias.pucher@wcl.ac.at>
Diff between staRdom versions 1.1.14 dated 2020-07-28 and 1.1.18 dated 2020-11-25
DESCRIPTION | 22 - MD5 | 62 ++-- R/absorption_functions.R | 13 R/correction_functions.R | 14 - R/eem_importers.R | 14 - R/parafac_functions.R | 45 +-- R/parafac_plot_functions.R | 13 README | 16 + build/vignette.rds |binary inst/doc/Basic_analysis_of_DOM_samples.Rmd | 8 inst/doc/Basic_analysis_of_DOM_samples.html | 60 ++++ inst/doc/PARAFAC_analysis_of_EEM.Rmd | 2 inst/doc/PARAFAC_analysis_of_EEM.html | 371 ++++++++++++++++------------ man/abs_blcor.Rd | 3 man/abs_parms.Rd | 6 man/eem_csv2.Rd | 6 man/eem_extend2largest.Rd | 2 man/eem_hitachi.Rd | 6 man/eem_interp.Rd | 12 man/eem_parafac.Rd | 3 man/eempf4analysis.Rd | 5 man/eempf_eemqual.Rd | 8 man/eempf_reorder.Rd | 2 man/eempf_report.Rd | 9 man/eempf_residuals.Rd | 2 man/eempf_residuals_plot.Rd | 2 man/eempf_varimp.Rd | 2 man/parafac_conv.Rd | 3 man/splithalf.Rd | 2 man/tcc_find_pairs.Rd | 2 vignettes/Basic_analysis_of_DOM_samples.Rmd | 8 vignettes/PARAFAC_analysis_of_EEM.Rmd | 2 32 files changed, 434 insertions(+), 291 deletions(-)
More information about ResearchAssociate at CRAN
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More information about DatastreamDSWS2R at CRAN
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Title: Stratified and Personalised Models Based on Model-Based Trees
and Forests
Description: Model-based trees for subgroup analyses in clinical trials and
model-based forests for the estimation and prediction of personalised
treatment effects (personalised models). Currently partitioning of linear
models, lm(), generalised linear models, glm(), and Weibull models,
survreg(), is supported. Advanced plotting functionality is supported for
the trees and a test for parameter heterogeneity is provided for the
personalised models. For details on model-based trees for subgroup analyses
see Seibold, Zeileis and Hothorn (2016) <doi:10.1515/ijb-2015-0032>; for
details on model-based forests for estimation of individual treatment effects
see Seibold, Zeileis and Hothorn (2017) <doi:10.1177/0962280217693034>.
Author: Heidi Seibold [aut, cre],
Achim Zeileis [aut],
Torsten Hothorn [aut]
Maintainer: Heidi Seibold <heidi@seibold.co>
Diff between model4you versions 0.9-5 dated 2020-02-19 and 0.9-6 dated 2020-11-25
DESCRIPTION | 10 ++-- MD5 | 42 ++++++++++---------- R/helpers.R | 11 +++-- R/plot-pmtree.R | 14 ++++-- R/pmodel.R | 6 ++ R/pmtree-methods.R | 3 - inst/NEWS.Rd | 12 +++++ man/binomial_glm_plot.Rd | 9 +++- man/lm_plot.Rd | 9 +++- man/logLik.pmtree.Rd | 3 - man/node_pmterminal.Rd | 12 ++++- man/objfun.Rd | 3 - man/objfun.pmtree.Rd | 3 - man/pmforest.Rd | 24 +++++++---- man/pmodel.Rd | 12 ++++- man/pmtree.Rd | 10 +++- man/predict.pmtree.Rd | 10 +++- man/print.pmtree.Rd | 10 +++- man/survreg_plot.Rd | 3 - man/varimp.pmforest.Rd | 10 +++- tests/test-pmtree.R | 14 +++--- tests/test-pmtree.Rout.save | 90 ++++++-------------------------------------- 22 files changed, 166 insertions(+), 154 deletions(-)
Title: Tools for Easier Analysis of Meteorological Fields
Description: Many useful functions and extensions for dealing
with meteorological data in the tidy data framework. Extends 'ggplot2'
for better plotting of scalar and vector fields and provides commonly
used analysis methods in the atmospheric sciences.
Author: Elio Campitelli [cre, aut] (<https://orcid.org/0000-0002-7742-9230>)
Maintainer: Elio Campitelli <elio.campitelli@cima.fcen.uba.ar>
Diff between metR versions 0.8.0 dated 2020-10-25 and 0.9.0 dated 2020-11-25
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Title: Diffusion Model of Conflict (DMC) in Reaction Time Tasks
Description: DMC model simulation detailed in Ulrich, R., Schroeter, H., Leuthold, H., & Birngruber, T. (2015).
Automatic and controlled stimulus processing in conflict tasks: Superimposed diffusion processes and delta functions.
Cognitive Psychology, 78, 148-174. Ulrich et al. (2015) <doi:10.1016/j.cogpsych.2015.02.005>.
Decision processes within choice reaction-time (CRT) tasks are often modelled using evidence accumulation models (EAMs),
a variation of which is the Diffusion Decision Model (DDM, for a review, see Ratcliff & McKoon, 2008).
Ulrich et al. (2015) introduced a Diffusion Model for Conflict tasks (DMC). The DMC model combines common
features from within standard diffusion models with the addition of superimposed controlled and automatic activation.
The DMC model is used to explain distributional reaction time (and error rate) patterns in common behavioural
conflict-like tasks (e.g., Flanker task, Simon task). This R-package implements the DMC model and provides functionality
to fit the model to observed data.
Author: Mackenzie G. Ian [cre, aut]
Maintainer: Mackenzie G. Ian <ian.mackenzie@uni-tuebingen.de>
Diff between DMCfun versions 0.15.0 dated 2020-09-20 and 1.1.0 dated 2020-11-25
DMCfun-0.15.0/DMCfun/man/dmcFitAgg.Rd |only DMCfun-0.15.0/DMCfun/man/dmcFitVPs.Rd |only DMCfun-0.15.0/DMCfun/man/mean.dmcfitvp.Rd |only DMCfun-0.15.0/DMCfun/man/plot.dmcfitvp.Rd |only DMCfun-0.15.0/DMCfun/man/summary.dmcfitvp.Rd |only DMCfun-0.15.0/DMCfun/tests/testthat/test-dmcFitAgg.R |only DMCfun-0.15.0/DMCfun/tests/testthat/test-dmcFitVPs.R |only DMCfun-1.1.0/DMCfun/DESCRIPTION | 26 DMCfun-1.1.0/DMCfun/MD5 | 114 +- DMCfun-1.1.0/DMCfun/NAMESPACE | 5 DMCfun-1.1.0/DMCfun/R/DMCfun.R | 4 DMCfun-1.1.0/DMCfun/R/dmcData.R | 250 ++-- DMCfun-1.1.0/DMCfun/R/dmcFit.R | 567 +++++++--- DMCfun-1.1.0/DMCfun/R/dmcSim.R | 20 DMCfun-1.1.0/DMCfun/R/plot.R | 772 +++++++++----- DMCfun-1.1.0/DMCfun/R/summary.R | 60 - DMCfun-1.1.0/DMCfun/R/zzz.R | 15 DMCfun-1.1.0/DMCfun/README.md | 41 DMCfun-1.1.0/DMCfun/data/flankerData.rda |binary DMCfun-1.1.0/DMCfun/data/flankerData.txt | 2 DMCfun-1.1.0/DMCfun/data/flankerDataRaw.rda |binary DMCfun-1.1.0/DMCfun/data/simonData.rda |binary DMCfun-1.1.0/DMCfun/data/simonData.txt | 2 DMCfun-1.1.0/DMCfun/data/simonDataRaw.rda |binary DMCfun-1.1.0/DMCfun/man/DMCfun-package.Rd | 22 DMCfun-1.1.0/DMCfun/man/addDataDF.Rd | 11 DMCfun-1.1.0/DMCfun/man/addErrorBars.Rd | 2 DMCfun-1.1.0/DMCfun/man/calculateCAF.Rd | 15 DMCfun-1.1.0/DMCfun/man/calculateCostValue.Rd | 2 DMCfun-1.1.0/DMCfun/man/calculateDelta.Rd | 13 DMCfun-1.1.0/DMCfun/man/createDF.Rd | 12 DMCfun-1.1.0/DMCfun/man/dmcCombineObservedData.Rd |only DMCfun-1.1.0/DMCfun/man/dmcFit.Rd |only DMCfun-1.1.0/DMCfun/man/dmcFitDE.Rd |only DMCfun-1.1.0/DMCfun/man/dmcFitSubject.Rd |only DMCfun-1.1.0/DMCfun/man/dmcFitSubjectDE.Rd |only DMCfun-1.1.0/DMCfun/man/dmcObservedData.Rd | 33 DMCfun-1.1.0/DMCfun/man/dmcSim.Rd | 6 DMCfun-1.1.0/DMCfun/man/dmcSims.Rd | 2 DMCfun-1.1.0/DMCfun/man/errDist.Rd | 2 DMCfun-1.1.0/DMCfun/man/flankerData.Rd | 3 DMCfun-1.1.0/DMCfun/man/flankerDataRaw.Rd | 2 DMCfun-1.1.0/DMCfun/man/mean.dmcfit.Rd |only DMCfun-1.1.0/DMCfun/man/plot.dmcfit.Rd | 15 DMCfun-1.1.0/DMCfun/man/plot.dmclist.Rd | 13 DMCfun-1.1.0/DMCfun/man/plot.dmcob.Rd | 23 DMCfun-1.1.0/DMCfun/man/plot.dmcobs.Rd |only DMCfun-1.1.0/DMCfun/man/plot.dmcsim.Rd | 6 DMCfun-1.1.0/DMCfun/man/rtDist.Rd | 2 DMCfun-1.1.0/DMCfun/man/simonDataRaw.Rd | 2 DMCfun-1.1.0/DMCfun/man/summary.dmcfit.Rd | 4 DMCfun-1.1.0/DMCfun/man/summary.dmcsim.Rd | 3 DMCfun-1.1.0/DMCfun/src/dmcCppR.cpp | 2 DMCfun-1.1.0/DMCfun/src/inDMC.cpp | 2 DMCfun-1.1.0/DMCfun/src/inDMC.h | 2 DMCfun-1.1.0/DMCfun/src/runDMC.cpp | 22 DMCfun-1.1.0/DMCfun/src/runDMC.h | 4 DMCfun-1.1.0/DMCfun/tests/testthat/test-addDataDF.R | 34 DMCfun-1.1.0/DMCfun/tests/testthat/test-calculateCAF.R | 16 DMCfun-1.1.0/DMCfun/tests/testthat/test-createDF.R | 14 DMCfun-1.1.0/DMCfun/tests/testthat/test-dmcFit.R |only DMCfun-1.1.0/DMCfun/tests/testthat/test-dmcFitSubject.R |only DMCfun-1.1.0/DMCfun/tests/testthat/test-dmcObservedData.R | 4 DMCfun-1.1.0/DMCfun/tests/testthat/test-dmcSim.R | 66 - DMCfun-1.1.0/DMCfun/tests/testthat/test-plot.dmcfit.R | 30 DMCfun-1.1.0/DMCfun/tests/testthat/test-plot.dmcob.R | 10 66 files changed, 1410 insertions(+), 867 deletions(-)
Title: 'Lua'-Filters for R Markdown
Description: A collection of 'Lua' filters that extend the functionality
of R Markdown templates (e.g., count words or post-process citations).
Author: Frederik Aust [aut, cre] (<https://orcid.org/0000-0003-4900-788X>),
Marius Barth [ctb]
Maintainer: Frederik Aust <frederik.aust@uni-koeln.de>
Diff between rmdfiltr versions 0.1.2 dated 2019-12-11 and 0.1.3 dated 2020-11-25
DESCRIPTION | 17 - LICENSE | 2 MD5 | 30 +-- NEWS.md | 6 R/add_lua_filter.R | 8 README.md | 2 build/vignette.rds |binary inst/WORDLIST | 7 inst/doc/replace_ampersands.Rmd | 12 - inst/doc/replace_ampersands.html | 259 ++++---------------------- inst/doc/wordcount.Rmd | 16 - inst/doc/wordcount.html | 269 +++++----------------------- inst/replace_ampersands.lua | 35 +++ tests/testthat/test_convenience_functions.R | 10 - vignettes/replace_ampersands.Rmd | 12 - vignettes/wordcount.Rmd | 16 - 16 files changed, 204 insertions(+), 497 deletions(-)
Title: Create Reports Using R and 'asciidoc'
Description: Inspired by Karl Broman`s reader on using 'knitr'
with 'asciidoc'
(<http://kbroman.org/knitr_knutshell/pages/asciidoc.html>), this is
merely a wrapper to 'knitr' and 'asciidoc'.
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between rasciidoc versions 2.2.1 dated 2020-11-18 and 2.2.2 dated 2020-11-25
DESCRIPTION | 6 MD5 | 47 +- NEWS.md | 10 R/highr_internals.R | 39 +- R/internals.R | 43 +- R/knitr_internals.R | 27 - R/knitr_internals_mod.R | 67 +-- R/render.R | 64 ++- R/throw.R | 2 R/vignette_engine.R | 16 R/zzz.R | 10 README.md | 9 inst/doc/An_Introduction_to_rasciidoc.Rasciidoc | 2 inst/doc/An_Introduction_to_rasciidoc.html | 60 +-- inst/files/default.html |only inst/runit_tests/files/expected/no_source_highlight |only inst/runit_tests/files/simple.asciidoc |only inst/runit_tests/runit-extraction.R | 14 inst/runit_tests/runit-highr_internals.R | 2 inst/runit_tests/runit-knitr_internals_mod.R | 56 +-- inst/runit_tests/runit-render.R | 350 +++++++++++--------- man/rasciidoc.Rd | 13 man/render.Rd | 4 man/throw.Rd | 2 tests/runit.R | 12 vignettes/An_Introduction_to_rasciidoc.Rasciidoc | 2 26 files changed, 471 insertions(+), 386 deletions(-)
Title: Efficient Computation of Ordinary and Generalized Poisson
Binomial Distributions
Description: Efficient implementations of multiple exact and approximate methods as described in Hong (2013) <doi:10.1016/j.csda.2012.10.006>, Biscarri, Zhao & Brunner (2018) <doi:10.1016/j.csda.2018.01.007> and Zhang, Hong & Balakrishnan (2018) <doi:10.1080/00949655.2018.1440294> for computing the probability mass, cumulative distribution and quantile functions, as well as generating random numbers for both the ordinary and generalized Poisson binomial distribution.
Author: Florian Junge [aut, cre]
Maintainer: Florian Junge <florian.junge@h-da.de>
Diff between PoissonBinomial versions 1.1.3 dated 2020-09-07 and 1.2.0 dated 2020-11-25
DESCRIPTION | 9 MD5 | 56 +- NAMESPACE | 1 NEWS.md | 13 R/RcppExports.R | 12 R/gpbinom.R | 744 ++++++++++++++--------------- R/pbinom.R | 64 ++ R/utility.R | 183 +++---- build/vignette.rds |binary inst/doc/intro.R | 69 +- inst/doc/intro.Rmd | 447 ++++++++--------- inst/doc/intro.html | 244 +++++---- inst/doc/proc_approx.R | 6 inst/doc/proc_approx.Rmd | 14 inst/doc/proc_approx.html | 94 ++- inst/doc/proc_exact.R | 10 inst/doc/proc_exact.Rmd | 18 inst/doc/proc_exact.html | 114 +++- inst/doc/use_with_rcpp.Rmd | 160 ++++-- inst/doc/use_with_rcpp.html | 208 ++++++-- inst/include/PoissonBinomial_RcppExports.h | 159 ++++-- man/GenPoissonBinomial-Distribution.Rd | 26 - man/PoissonBinomial-Distribution.Rd | 19 src/PoissonBinomial.cpp | 727 +++++++++++++++++----------- src/RcppExports.cpp | 369 +++++++++----- vignettes/intro.Rmd | 447 ++++++++--------- vignettes/proc_approx.Rmd | 14 vignettes/proc_exact.Rmd | 18 vignettes/use_with_rcpp.Rmd | 160 ++++-- 29 files changed, 2629 insertions(+), 1776 deletions(-)
More information about PoissonBinomial at CRAN
Permanent link
Title: Periodic Autoregressive Time Series Models
Description: Basic functions to fit and predict periodic autoregressive time series models. These models are discussed in the book P.H. Franses (1996) "Periodicity and Stochastic Trends in Economic Time Series", Oxford University Press. Data set analyzed in that book is also provided. NOTE: the package was orphaned during several years. It is now only maintained, but no major enhancements are expected, and the maintainer cannot provide any support.
Author: Javier Lopez-de-Lacalle [aut, cph],
Matthieu Stigler [cre] (<https://orcid.org/0000-0002-6802-4290>)
Maintainer: Matthieu Stigler <Matthieu.Stigler@gmail.com>
Diff between partsm versions 1.1-2 dated 2014-03-31 and 1.1-3 dated 2020-11-25
DESCRIPTION | 29 ++++-- MD5 | 116 ++++++++++++------------- NAMESPACE | 9 + R/bbplot.R | 6 - R/partsm.R | 8 - build/vignette.rds |binary data/canun.rda |binary data/canunsa.rda |binary data/gergnp.rda |binary data/gergnpsa.rda |binary data/swdipc.rda |binary data/swndcpc.rda |binary data/ukcons.rda |binary data/ukexp.rda |binary data/ukgdp.rda |binary data/ukimp.rda |binary data/ukinvest.rda |binary data/ukndcons.rda |binary data/ukpinvest.rda |binary data/ukwf.rda |binary data/usaipi.rda |binary data/usaipisa.rda |binary inst/ChangeLog | 4 inst/WORDLIST |only inst/doc/partsm.Rnw | 18 +-- inst/doc/partsm.pdf |binary inst/internal_tests_devtools.R |only man/Fnextp.test.Rd | 2 man/Fpar.test.Rd | 2 man/Fpari.piar.test.Rd | 5 - man/LRur.partsm-class.Rd | 2 man/LRurpar.test.Rd | 6 - man/MVPAR-class.Rd | 6 - man/MVPIAR-class.Rd | 6 - man/PAR.MVrepr-method.Rd | 2 man/canun.Rd | 2 man/canunsa.Rd | 2 man/fit.piar.Rd | 4 man/fit.piartsm-class.Rd | 2 man/gergnp.Rd | 2 man/gergnpsa.Rd | 2 man/plotpredpiar.Rd | 2 man/pred.piartsm-class.Rd | 2 man/predictpiar.Rd | 3 man/swdipc.Rd | 2 man/swndcpc.Rd | 2 man/ukcons.Rd | 2 man/ukexp.Rd | 2 man/ukgdp.Rd | 2 man/ukimp.Rd | 2 man/ukinvest.Rd | 2 man/ukndcons.Rd | 2 man/ukpinvest.Rd | 2 man/ukwf.Rd | 3 man/usaipi.Rd | 2 man/usaipisa.Rd | 2 tests/partsm_examples.R | 4 tests/partsm_examples.Rout.save | 182 ++++++++++++++++++++-------------------- vignettes/partsm.Rnw | 18 +-- vignettes/partsm.cls | 2 60 files changed, 247 insertions(+), 226 deletions(-)
Title: General Equilibrium Modeling
Description: Some tools for developing general equilibrium models and some general equilibrium models. These models can be used for teaching economic theory and are built by the methods of new structural economics (see <https://www.nse.pku.edu.cn/> and LI Wu, 2019, ISBN: 9787521804225, General Equilibrium and Structural Dynamics: Perspectives of New Structural Economics. Beijing: Economic Science Press). The model form and mathematical methods can be traced back to von Neumann, J. (1945, A Model of General Economic Equilibrium. The Review of Economic Studies, 13. pp. 1-9) and Kemeny, J. G., O. Morgenstern and G. L. Thompson (1956, A Generalization of the von Neumann Model of an Expanding Economy, Econometrica, 24, pp. 115-135) et al. By the way, J. G. Kemeny is a co-inventor of the computer language BASIC.
Author: LI Wu <liwu@staff.shu.edu.cn>
Maintainer: LI Wu <liwu@staff.shu.edu.cn>
Diff between GE versions 0.1.4 dated 2020-06-11 and 0.1.6 dated 2020-11-25
DESCRIPTION | 6 ++--- MD5 | 28 +++++++++++++------------ NAMESPACE | 1 R/CES.R | 8 +++++-- R/gemCanonicalDynamicMacroeconomic_3_2.R | 1 R/gemDualLinearProgramming.R | 14 ++++++------ R/gemQuasilinearPureExchange_2_2.R | 31 ++++++++++++++++++++++++++++ R/gemRobinson_3_2.R | 6 ++--- R/gemTwoCountryPureExchange_Bond.R |only R/sdm2.R | 6 +++-- man/gemCanonicalDynamicMacroeconomic_3_2.Rd | 3 ++ man/gemDualLinearProgramming.Rd | 14 ++++++------ man/gemQuasilinearPureExchange_2_2.Rd | 31 ++++++++++++++++++++++++++++ man/gemRobinson_3_2.Rd | 6 ++--- man/gemTwoCountryPureExchange_Bond.Rd |only man/sdm2.Rd | 2 - 16 files changed, 116 insertions(+), 41 deletions(-)
Title: Collect ESPN Fantasy Football Data
Description: Format the raw data from the ESPN fantasy football
API <https://fantasy.espn.com/apis/v3/games/ffl/> into tidy tables.
Scrape data on public leagues, rosters, athletes, and matches.
Author: Kiernan Nicholls [aut, cre]
Maintainer: Kiernan Nicholls <kiernann@protonmail.com>
Diff between fflr versions 0.3.12 dated 2020-11-06 and 0.3.13 dated 2020-11-25
DESCRIPTION | 8 MD5 | 44 - NEWS.md | 8 R/all-players.R | 8 R/live-scoring.R | 1 R/match-schedule.R | 2 R/match-scores.R | 2 R/player-outlook.R | 7 R/pro-schedule.R | 1 R/roster-moves.R | 1 R/week-scores.R | 2 README.md | 130 ++-- build/vignette.rds |binary inst/doc/fantasy-football.R | 12 inst/doc/fantasy-football.Rmd | 24 inst/doc/fantasy-football.html | 1036 +++++++++++++++++------------------ man/all_players.Rd | 6 man/figures/README-plot_scores-1.png |binary man/player_outlook.Rd | 6 tests/testthat/test-moves.R | 2 tests/testthat/test-outlooks.R | 2 tests/testthat/test-players.R | 7 vignettes/fantasy-football.Rmd | 24 23 files changed, 672 insertions(+), 661 deletions(-)
Title: Estimation of the Proportion of SB Explained by Confounders
Description: Uses parametric and nonparametric methods to quantify the proportion of the estimated selection bias (SB) explained by each observed confounder when estimating propensity score weighted treatment effects. Parast, L and Griffin, BA (2020). "Quantifying the Bias due to Observed Individual Confounders in Causal Treatment Effect Estimates". Statistics in Medicine, 39(18): 2447- 2476 <doi: 10.1002/sim.8549>.
Author: Layla Parast
Maintainer: Layla Parast <parast@rand.org>
Diff between SBdecomp versions 1.0 dated 2020-05-12 and 1.1 dated 2020-11-25
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- R/SBdecomp.R | 18 ++++++++++++------ build/partial.rdb |binary data/petsdata.RData |binary man/SBdecomp-package.Rd | 2 +- man/bar.sbdecomp.Rd | 2 +- man/sbdecomp.Rd | 4 +++- 9 files changed, 31 insertions(+), 23 deletions(-)
Title: Versatile Curation of Table Metadata
Description: A file-based
mechanism for documenting datasets. It reads and writes
YAML-formatted metadata and applies it as data
item attributes. Data and metadata are stored independently
but can be coordinated by using similar file paths with
different extensions. The 'yamlet' dialect is valid 'YAML',
but some conventions are chosen to improve readability.
Defaults and conventions can be over-ridden by the user.
See ?yamlet and ?decorate.data.frame.
See ?read_yamlet ?write_yamlet, and ?io_csv.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between yamlet versions 0.5.1 dated 2020-11-24 and 0.5.2 dated 2020-11-25
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/decorate.R | 2 +- R/explicit_guide.R | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Tidy Data Validation Reports
Description: Tools for creating data validation pipelines and
tidy reports. This package offers a framework for exploring and
validating data frame like objects using 'dplyr' grammar of data
manipulation.
Author: Evgeni Chasnovski [aut, cre] (<https://orcid.org/0000-0002-1617-4019>)
Maintainer: Evgeni Chasnovski <evgeni.chasnovski@gmail.com>
Diff between ruler versions 0.2.3 dated 2020-05-09 and 0.2.4 dated 2020-11-25
ruler-0.2.3/ruler/man/reexports.Rd |only ruler-0.2.4/ruler/DESCRIPTION | 16 ruler-0.2.4/ruler/MD5 | 107 +- ruler-0.2.4/ruler/NAMESPACE | 1 ruler-0.2.4/ruler/NEWS.md | 4 ruler-0.2.4/ruler/R/actions.R | 31 ruler-0.2.4/ruler/R/expose-helpers.R | 36 ruler-0.2.4/ruler/R/expose.R | 102 +- ruler-0.2.4/ruler/R/exposure.R | 85 + ruler-0.2.4/ruler/R/packs.R | 54 - ruler-0.2.4/ruler/R/ruler-package.R | 2 ruler-0.2.4/ruler/R/rules.R | 15 ruler-0.2.4/ruler/R/spread-groups.R | 24 ruler-0.2.4/ruler/R/utils-pipe.R |only ruler-0.2.4/ruler/R/utils.R | 5 ruler-0.2.4/ruler/README.md | 111 +- ruler-0.2.4/ruler/build/vignette.rds |binary ruler-0.2.4/ruler/inst/doc/design-and-format.Rmd | 6 ruler-0.2.4/ruler/inst/doc/design-and-format.html | 370 +++---- ruler-0.2.4/ruler/inst/doc/rule-packs.R | 18 ruler-0.2.4/ruler/inst/doc/rule-packs.Rmd | 26 ruler-0.2.4/ruler/inst/doc/rule-packs.html | 749 +++++++-------- ruler-0.2.4/ruler/inst/doc/validation.R | 12 ruler-0.2.4/ruler/inst/doc/validation.Rmd | 16 ruler-0.2.4/ruler/inst/doc/validation.html | 799 +++++++---------- ruler-0.2.4/ruler/man/act_after_exposure.Rd | 6 ruler-0.2.4/ruler/man/any_breaker.Rd | 1 ruler-0.2.4/ruler/man/assert_any_breaker.Rd | 6 ruler-0.2.4/ruler/man/bind_exposures.Rd | 16 ruler-0.2.4/ruler/man/cell-pack.Rd | 8 ruler-0.2.4/ruler/man/column-pack.Rd | 7 ruler-0.2.4/ruler/man/data-pack.Rd | 14 ruler-0.2.4/ruler/man/expose.Rd | 33 ruler-0.2.4/ruler/man/exposure.Rd | 3 ruler-0.2.4/ruler/man/group-pack.Rd | 12 ruler-0.2.4/ruler/man/inside_punct.Rd | 1 ruler-0.2.4/ruler/man/packs_info.Rd | 11 ruler-0.2.4/ruler/man/pipe.Rd |only ruler-0.2.4/ruler/man/row-pack.Rd | 12 ruler-0.2.4/ruler/man/rule-packs.Rd | 2 ruler-0.2.4/ruler/man/ruler-package.Rd | 4 ruler-0.2.4/ruler/man/ruler-report.Rd | 11 ruler-0.2.4/ruler/man/rules.Rd | 17 ruler-0.2.4/ruler/man/spread_groups.Rd | 1 ruler-0.2.4/ruler/tests/testthat/helper-expose-data.R | 69 - ruler-0.2.4/ruler/tests/testthat/test-actions.R | 163 ++- ruler-0.2.4/ruler/tests/testthat/test-expose-helpers.R | 64 - ruler-0.2.4/ruler/tests/testthat/test-expose.R | 183 ++- ruler-0.2.4/ruler/tests/testthat/test-exposure.R | 116 +- ruler-0.2.4/ruler/tests/testthat/test-packs.R | 61 - ruler-0.2.4/ruler/tests/testthat/test-rules.R | 8 ruler-0.2.4/ruler/tests/testthat/test-spread-groups.R | 64 - ruler-0.2.4/ruler/tests/testthat/test-utils.R | 65 - ruler-0.2.4/ruler/vignettes/design-and-format.Rmd | 6 ruler-0.2.4/ruler/vignettes/rule-packs.Rmd | 26 ruler-0.2.4/ruler/vignettes/validation.Rmd | 16 56 files changed, 1887 insertions(+), 1708 deletions(-)
Title: Linking Patient-Reported Outcomes Measures
Description: Perform scale linking to establish relationships between instruments
that measure similar constructs according to the PROsetta Stone methodology, as in Choi, Schalet, Cook, & Cella (2014) <doi:10.1037/a0035768>.
Author: Seung W. Choi [aut, cre] (<https://orcid.org/0000-0003-4777-5420>),
Sangdon Lim [aut] (<https://orcid.org/0000-0002-2988-014X>),
Benjamin D. Schalet [ctb],
Aaron J. Kaat [ctb],
David Cella [ctb]
Maintainer: Seung W. Choi <schoi@austin.utexas.edu>
Diff between PROsetta versions 0.2.0 dated 2020-09-20 and 0.2.1 dated 2020-11-25
PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/alpha2_3f4081608d050ce976ddb7b5e1e0a683.RData |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/alpha2_3f4081608d050ce976ddb7b5e1e0a683.rdb |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/alpha2_3f4081608d050ce976ddb7b5e1e0a683.rdx |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/alpha_0345803d49f27d51c0f3ee5f687f2f78.RData |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/alpha_0345803d49f27d51c0f3ee5f687f2f78.rdb |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/alpha_0345803d49f27d51c0f3ee5f687f2f78.rdx |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/calib2_844987e1c44a4c824f7b788bff95f10a.RData |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/calib2_844987e1c44a4c824f7b788bff95f10a.rdb |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/calib2_844987e1c44a4c824f7b788bff95f10a.rdx |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/calib3_6dde06c6cc4ba29bea07e63fd415b9c5.RData |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/calib3_6dde06c6cc4ba29bea07e63fd415b9c5.rdb |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/calib3_6dde06c6cc4ba29bea07e63fd415b9c5.rdx |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/calib_1b7d905f90d92418f2819759c4d06ed9.RData |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/calib_1b7d905f90d92418f2819759c4d06ed9.rdb |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/calib_1b7d905f90d92418f2819759c4d06ed9.rdx |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/eqp_dir_fd943eec124845a64bc09100a57df1b5.RData |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/eqp_dir_fd943eec124845a64bc09100a57df1b5.rdb |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/eqp_dir_fd943eec124845a64bc09100a57df1b5.rdx |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/eqp_raw_9de97fff5c190503715b2e27d2db4316.RData |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/eqp_raw_9de97fff5c190503715b2e27d2db4316.rdb |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/eqp_raw_9de97fff5c190503715b2e27d2db4316.rdx |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/fixedpar_15e265aedc8d1e97f5d2afdfc0e135ae.RData |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/fixedpar_15e265aedc8d1e97f5d2afdfc0e135ae.rdb |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/fixedpar_15e265aedc8d1e97f5d2afdfc0e135ae.rdx |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/mirt_coef_ed17672a8b6a43aa2db9e2eedbbd3f85.RData |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/mirt_coef_ed17672a8b6a43aa2db9e2eedbbd3f85.rdb |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/mirt_coef_ed17672a8b6a43aa2db9e2eedbbd3f85.rdx |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/mirt_plot_3005f6253c69ecaf2a58412637b4f595.RData |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/mirt_plot_3005f6253c69ecaf2a58412637b4f595.rdb |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/mirt_plot_3005f6253c69ecaf2a58412637b4f595.rdx |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/omega_7e75d3a862efc4baa2025fe197929cbe.RData |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/omega_7e75d3a862efc4baa2025fe197929cbe.rdb |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/omega_7e75d3a862efc4baa2025fe197929cbe.rdx |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/sl_456fd2904030e8839f5e74483b8098bd.RData |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/sl_456fd2904030e8839f5e74483b8098bd.rdb |only PROsetta-0.2.0/PROsetta/vignettes/PROsetta_cache/html/sl_456fd2904030e8839f5e74483b8098bd.rdx |only PROsetta-0.2.1/PROsetta/DESCRIPTION | 14 PROsetta-0.2.1/PROsetta/MD5 | 89 +-- PROsetta-0.2.1/PROsetta/NAMESPACE | 2 PROsetta-0.2.1/PROsetta/NEWS.md | 7 PROsetta-0.2.1/PROsetta/R/core_functions.R | 10 PROsetta-0.2.1/PROsetta/R/helper_functions.R |only PROsetta-0.2.1/PROsetta/README.md | 3 PROsetta-0.2.1/PROsetta/build/vignette.rds |binary PROsetta-0.2.1/PROsetta/inst/doc/PROsetta.html | 241 +++++----- PROsetta-0.2.1/PROsetta/man/getItemNames.Rd |only PROsetta-0.2.1/PROsetta/man/getResponse.Rd |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/alpha2_a29946f4f5d0cca3dc3e255562932092.RData |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/alpha2_a29946f4f5d0cca3dc3e255562932092.rdb |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/alpha2_a29946f4f5d0cca3dc3e255562932092.rdx |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/alpha_0409ebb27b7b72ee7aac176ef3d5dd88.RData |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/alpha_0409ebb27b7b72ee7aac176ef3d5dd88.rdb |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/alpha_0409ebb27b7b72ee7aac176ef3d5dd88.rdx |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/calib2_cbb4e7866403c21020e42df79fe1bde7.RData |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/calib2_cbb4e7866403c21020e42df79fe1bde7.rdb |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/calib2_cbb4e7866403c21020e42df79fe1bde7.rdx |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/calib3_1b30cb5058fe0279ae7ff20574ed2586.RData |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/calib3_1b30cb5058fe0279ae7ff20574ed2586.rdb |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/calib3_1b30cb5058fe0279ae7ff20574ed2586.rdx |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/calib_0040d330a2b33c47e7db550ad22aa890.RData |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/calib_0040d330a2b33c47e7db550ad22aa890.rdb |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/calib_0040d330a2b33c47e7db550ad22aa890.rdx |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/eqp_dir_0aa9c1a4fb1402cc4e4d2f22c9eaf1c2.RData |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/eqp_dir_0aa9c1a4fb1402cc4e4d2f22c9eaf1c2.rdb |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/eqp_dir_0aa9c1a4fb1402cc4e4d2f22c9eaf1c2.rdx |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/eqp_raw_315c3d82bd5303c670647e036326e823.RData |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/eqp_raw_315c3d82bd5303c670647e036326e823.rdb |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/eqp_raw_315c3d82bd5303c670647e036326e823.rdx |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/fixedpar_71d37083af79eb9abbfa06beaf96d65f.RData |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/fixedpar_71d37083af79eb9abbfa06beaf96d65f.rdb |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/fixedpar_71d37083af79eb9abbfa06beaf96d65f.rdx |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/mirt_coef_122868579fa6981caaeab7c705f3ba4d.RData |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/mirt_coef_122868579fa6981caaeab7c705f3ba4d.rdb |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/mirt_coef_122868579fa6981caaeab7c705f3ba4d.rdx |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/mirt_plot_87d971052f5c887a53cb87f7a1bab877.RData |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/mirt_plot_87d971052f5c887a53cb87f7a1bab877.rdb |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/mirt_plot_87d971052f5c887a53cb87f7a1bab877.rdx |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/omega_cf19f74a8ba93cb71c27d26c413bd173.RData |only PROsetta-0.2.1/PROsetta/vignettes/PROsetta_cache/html/omega_cf19f74a8ba93cb71c27d26c413bd173.rdb |only 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Title: Tools and Statistical Procedures in Plant Science
Description: The 'inti' package is part of the 'inkaverse' project for developing
different procedures and tools used in plant science and experimental designs.
The mean aim of the package is to support researchers during the planning of
experiments and data collection (tarpuy()), data analysis and graphics (yupana())
, and technical writing (rtciles()).
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] (<https://orcid.org/0000-0002-0714-669X>)
Maintainer: Flavio Lozano-Isla <flavjack@gmail.com>
Diff between inti versions 0.1.1 dated 2020-11-17 and 0.1.2 dated 2020-11-25
inti-0.1.1/inti/inst/tarpuy/rsconnect/shinyapps.io/flavjack/tarpuy_test.dcf |only inti-0.1.1/inti/inst/yupanapro/rsconnect/shinyapps.io/flavjack/yupanapro_test.dcf |only inti-0.1.2/inti/DESCRIPTION | 16 +-- inti-0.1.2/inti/MD5 | 43 ++++------ inti-0.1.2/inti/NAMESPACE | 2 inti-0.1.2/inti/NEWS.md | 9 ++ inti-0.1.2/inti/R/H2cal.R | 1 inti-0.1.2/inti/R/include_table.R | 22 ++--- inti-0.1.2/inti/R/info_table.R | 4 inti-0.1.2/inti/R/outliers_remove.R | 32 ++++--- inti-0.1.2/inti/inst/rticles/rsconnect/shinyapps.io/flavjack/rticles.dcf | 4 inti-0.1.2/inti/inst/rticles/server.R | 3 inti-0.1.2/inti/inst/rticles/ui.R | 3 inti-0.1.2/inti/inst/tarpuy/rsconnect/shinyapps.io/flavjack/tarpuy-test.dcf |only inti-0.1.2/inti/inst/tarpuy/rsconnect/shinyapps.io/flavjack/tarpuy.dcf | 4 inti-0.1.2/inti/inst/tarpuy/server.R | 10 +- inti-0.1.2/inti/inst/tarpuy/ui.R | 5 - inti-0.1.2/inti/inst/yupanapro/rsconnect/shinyapps.io/flavjack/yupanapro.dcf | 4 inti-0.1.2/inti/inst/yupanapro/server.R | 27 +++--- inti-0.1.2/inti/inst/yupanapro/ui.R | 5 - inti-0.1.2/inti/man/H2cal.Rd | 1 inti-0.1.2/inti/man/include_table.Rd | 4 inti-0.1.2/inti/man/info_table.Rd | 4 inti-0.1.2/inti/man/outliers_remove.Rd | 14 +++ 24 files changed, 123 insertions(+), 94 deletions(-)
Title: Cross-Validated Kernel Ensemble
Description: Implementation of Cross-Validated Kernel Ensemble (CVEK),
a flexible modeling framework for robust nonlinear regression and
hypothesis testing based on ensemble learning with kernel-ridge estimators
(Jeremiah et al. (2017) <arXiv:1710.01406> and
Wenying et al. (2018) <arXiv:1811.11025>). It allows user to conduct
nonlinear regression with minimal assumption on the function form by
aggregating nonlinear models generated from a diverse collection of kernel
families. It also provides utilities to test for the estimated nonlinear
effect under this ensemble estimator, using either the asymptotic or
the bootstrap version of a generalized score test.
Author: Wenying Deng [aut, cre],
Jeremiah Zhe Liu [ctb]
Maintainer: Wenying Deng <wdeng@g.harvard.edu>
Diff between CVEK versions 0.1-0 dated 2020-11-23 and 0.1-1 dated 2020-11-25
DESCRIPTION | 8 - MD5 | 30 +++---- R/interface.R | 1 R/predict.R | 1 inst/doc/vignette.R | 9 -- inst/doc/vignette.Rmd | 16 +-- inst/doc/vignette.html | 135 ++++++++++++++++----------------- man/cvek.Rd | 1 man/predict.cvek.Rd | 1 tests/testthat/helper_test_interface.R | 1 tests/testthat/test_est.R | 20 ++-- tests/testthat/test_hypo_test.R | 8 + tests/testthat/test_interface.R | 4 tests/testthat/test_kernel.R | 7 + tests/testthat/test_predict.R | 7 - vignettes/vignette.Rmd | 16 +-- 16 files changed, 139 insertions(+), 126 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-11 0.7.1
2019-09-03 0.7.0
2019-06-05 0.6.1
2019-05-23 0.6.0
2019-01-23 0.5.7
2018-11-15 0.5.6
2018-09-28 0.5.5
2018-05-16 0.5.4
2018-03-10 0.5.3
2018-02-13 0.5.2
2018-01-26 0.5.1
2018-01-05 0.5.0
Title: Advanced 'tryCatch()' and 'try()' Functions
Description: Advanced tryCatch() and try() functions for better error handling
(logging, stack trace with source code references and support for post-mortem analysis via dump files).
Author: Juergen Altfeld [aut, cre, cph],
Charles Epaillard [ctb],
Brandon Bertelsen [ctb]
Maintainer: Juergen Altfeld <jaltfeld@altfeld-im.de>
Diff between tryCatchLog versions 1.1.6 dated 2019-11-06 and 1.2.1 dated 2020-11-25
DESCRIPTION | 14 MD5 | 76 - NEWS.md | 50 R/build_log_entry.R | 27 R/build_log_output.R | 7 R/conditions.R |only R/is_duplicated_log_entry.R | 2 R/last_tryCatchLog_result.R | 20 R/log2console.R | 2 R/tryCatchLog.R | 193 ++- R/tryLog.R | 23 R/zzz.R | 2 inst/doc/01_license.Rmd_child | 2 inst/doc/02_toc.Rmd_child | 22 inst/doc/05_overview.Rmd_child | 12 inst/doc/10_standard_R_conditions.Rmd_child | 6 inst/doc/20_tryCatchLog.Rmd_child | 4 inst/doc/90_appendix.Rmd_child | 4 inst/doc/tryCatchLog-intro.R | 82 - inst/doc/tryCatchLog-intro.html | 1598 ++++++++++++-------------- man/build.log.entry.Rd | 18 man/build.log.output.Rd | 15 man/is.duplicated.log.entry.Rd | 2 man/last.tryCatchLog.result.Rd | 20 man/limitedLabelsCompact.Rd | 7 man/set.logging.functions.Rd | 9 man/tryCatchLog.Rd | 88 - man/tryLog.Rd | 42 tests/testthat/test_build_log_entry.R | 23 tests/testthat/test_build_log_output.R | 71 + tests/testthat/test_dump_files.R | 127 +- tests/testthat/test_execution_context_msg.R |only tests/testthat/test_interrupt.R |only tests/testthat/test_user_defined_conditions.R |only vignettes/01_license.Rmd_child | 2 vignettes/02_toc.Rmd_child | 22 vignettes/05_overview.Rmd_child | 12 vignettes/10_standard_R_conditions.Rmd_child | 6 vignettes/20_tryCatchLog.Rmd_child | 4 vignettes/90_appendix.Rmd_child | 4 vignettes/README_FIRST.txt | 8 41 files changed, 1429 insertions(+), 1197 deletions(-)
Title: Generate Standardized Data
Description: Creates simulated data from structural equation models with standardized loading. Data generation methods are described in Schneider (2013) <doi:10.1177/0734282913478046>.
Author: W. Joel Schneider [aut, cre] (<https://orcid.org/0000-0002-8393-5316>)
Maintainer: W. Joel Schneider <w.joel.schneider@gmail.com>
Diff between simstandard versions 0.5.0 dated 2020-10-22 and 0.6.0 dated 2020-11-25
DESCRIPTION | 6 - MD5 | 20 ++--- NAMESPACE | 2 NEWS.md | 3 R/main.R | 51 ++++++++++++ build/vignette.rds |binary inst/WORDLIST |only inst/doc/simstandard_tutorial.R | 13 ++- inst/doc/simstandard_tutorial.Rmd | 23 +++++ inst/doc/simstandard_tutorial.html | 135 +++++++++++++++------------------- man/get_model_implied_correlations.Rd |only vignettes/simstandard_tutorial.Rmd | 23 +++++ 12 files changed, 182 insertions(+), 94 deletions(-)
Title: Genetics and Independence Testing of Mixed Genetic Panels
Description: Developed to deal with multi-locus genotype data, this package is especially designed for those panel which include different type of markers. Basic genetic parameters like allele frequency, genotype frequency, heterozygosity and Hardy-Weinberg test of mixed genetic data can be obtained. In addition, a new test for mutual independence which is compatible for mixed genetic data is developed in this package.
Author: Bing Song
Maintainer: Bing Song <bingsong@my.unthsc.edu>
Diff between mixIndependR versions 0.3.0 dated 2020-10-07 and 0.4.0 dated 2020-11-25
mixIndependR-0.3.0/mixIndependR/R/AlleleShare_Table.R |only mixIndependR-0.3.0/mixIndependR/R/HWE_Fisher.R |only mixIndependR-0.3.0/mixIndependR/man/AlleleShare_Table.Rd |only mixIndependR-0.3.0/mixIndependR/man/HWE.Fisher.Rd |only mixIndependR-0.4.0/mixIndependR/DESCRIPTION | 10 mixIndependR-0.4.0/mixIndependR/MD5 | 82 mixIndependR-0.4.0/mixIndependR/NAMESPACE | 56 mixIndependR-0.4.0/mixIndependR/NEWS.md | 103 - mixIndependR-0.4.0/mixIndependR/R/AlleleFreq.R | 62 mixIndependR-0.4.0/mixIndependR/R/AlleleShare.R |only mixIndependR-0.4.0/mixIndependR/R/Dist_SimuChisq.R | 58 mixIndependR-0.4.0/mixIndependR/R/FreqAlleleShare.R | 39 mixIndependR-0.4.0/mixIndependR/R/FreqHetero.R | 39 mixIndependR-0.4.0/mixIndependR/R/GenotypeFreq.R | 102 - mixIndependR-0.4.0/mixIndependR/R/HWE_Chisq.R | 118 - mixIndependR-0.4.0/mixIndependR/R/Heterozygous.R | 62 mixIndependR-0.4.0/mixIndependR/R/RealProAlleleShare.R | 37 mixIndependR-0.4.0/mixIndependR/R/Simulate_DistK.R | 64 mixIndependR-0.4.0/mixIndependR/R/Simulate_DistX.R | 69 mixIndependR-0.4.0/mixIndependR/R/mixIndependK.R | 80 mixIndependR-0.4.0/mixIndependR/R/mixIndependX.R | 79 mixIndependR-0.4.0/mixIndependR/R/read_vcf_gt.R |only mixIndependR-0.4.0/mixIndependR/R/splitGenotype.R |only mixIndependR-0.4.0/mixIndependR/README.md | 59 mixIndependR-0.4.0/mixIndependR/build/vignette.rds |binary mixIndependR-0.4.0/mixIndependR/inst/doc/BasicGenetics.R | 95 mixIndependR-0.4.0/mixIndependR/inst/doc/BasicGenetics.Rmd | 164 - mixIndependR-0.4.0/mixIndependR/inst/doc/BasicGenetics.html | 1003 +++++----- mixIndependR-0.4.0/mixIndependR/inst/doc/DistributionBuildingNComparison.R | 98 mixIndependR-0.4.0/mixIndependR/inst/doc/DistributionBuildingNComparison.Rmd | 134 - mixIndependR-0.4.0/mixIndependR/inst/doc/DistributionBuildingNComparison.html | 796 ++++--- mixIndependR-0.4.0/mixIndependR/inst/doc/HypothesisTest.R | 82 mixIndependR-0.4.0/mixIndependR/inst/doc/HypothesisTest.Rmd | 114 - mixIndependR-0.4.0/mixIndependR/inst/doc/HypothesisTest.html | 742 +++---- mixIndependR-0.4.0/mixIndependR/man/AlleleFreq.Rd | 15 mixIndependR-0.4.0/mixIndependR/man/AlleleShare.Rd |only mixIndependR-0.4.0/mixIndependR/man/GenotypeFreq.Rd | 20 mixIndependR-0.4.0/mixIndependR/man/HWE.Chisq.Rd | 23 mixIndependR-0.4.0/mixIndependR/man/Heterozygous.Rd | 14 mixIndependR-0.4.0/mixIndependR/man/Simulate_DistX.Rd | 2 mixIndependR-0.4.0/mixIndependR/man/mixIndependK.Rd | 16 mixIndependR-0.4.0/mixIndependR/man/mixIndependX.Rd | 16 mixIndependR-0.4.0/mixIndependR/man/read_vcf_gt.Rd |only mixIndependR-0.4.0/mixIndependR/man/splitGenotype.Rd |only mixIndependR-0.4.0/mixIndependR/vignettes/BasicGenetics.Rmd | 164 - mixIndependR-0.4.0/mixIndependR/vignettes/DistributionBuildingNComparison.Rmd | 134 - mixIndependR-0.4.0/mixIndependR/vignettes/HypothesisTest.Rmd | 114 - 47 files changed, 2366 insertions(+), 2499 deletions(-)
Title: Bayesian Spatial Split Population Survival Model
Description: Parametric spatial split-population (SP) survival models for clustered
event processes. The models account for structural and spatial heterogeneity among
“at risk” and “immune” populations, and incorporate time-varying covariates.
This package currently implements Weibull, Exponential and Log-logistic forms for
the duration component. It also includes functions for a series of diagnostic
tests and plots to easily visualize spatial autocorrelation, convergence, and spatial effects. Users can
create their own spatial weights matrix based on their units and adjacencies of
interest, making the use of these models flexible and broadly applicable to a
variety of research areas. Joo et al. (2020) <https://github.com/Nicolas-Schmidt/BayesSPsurv/blob/master/man/figures/SPcure.pdf> describe
the estimators included in this package.
Author: Brandon L. Bolte [aut],
Nicolas Schmidt [aut, cre],
Sergio Bejar [aut],
Bumba Mukherjee [aut],
Minnie M. Joo [ctb],
Nguyen K. Huynh [ctb]
Maintainer: Nicolas Schmidt <nschmidt@cienciassociales.edu.uy>
Diff between BayesSPsurv versions 0.1.0 dated 2020-09-28 and 0.1.1 dated 2020-11-25
DESCRIPTION | 12 +++++---- MD5 | 24 +++++++++++-------- NAMESPACE | 2 + NEWS.md |only R/exchangeSPsurv.R | 2 - R/plots.R |only R/pooledSPsurv.R | 2 - R/spatialSPsurv.R | 2 - R/utils.R | 60 ++++++++++++++++++++++++++++++++++++++++++++++--- README.md | 12 +++++++-- man/exchangeSPsurv.Rd | 2 - man/plot_JointCount.Rd |only man/plot_Moran.I.Rd |only man/pooledSPsurv.Rd | 2 - man/spatialSPsurv.Rd | 2 - 15 files changed, 95 insertions(+), 27 deletions(-)
Title: UK Flood Estimation
Description: Functions to implement the methods of the Flood Estimation Handbook (FEH), associated updates and the revitalised flood hydrograph model (ReFH). Currently the packages uses NRFA peak flow dataset version 9. Aside from FEH functionality, further hydrological functions are available. Most of the methods implemented in this package are described in one or more of the following: "Flood Estimation Handbook", Centre for Ecology & Hydrology (1999, ISBN:0 948540 94 X). "Flood Estimation Handbook Supplementary Report No. 1", Kjeldsen (2007, ISBN:0 903741 15 7). "Regional Frequency Analysis - an approach based on L-moments", Hosking & Wallis (1997, ISBN: 978 0 521 01940 8). "Proposal of the ‘extreme rank plot’ for extreme value analysis: with an emphasis on flood frequency studies", Hammond (2019, <doi:10.2166/nh.2019.157>). "Making better use of local data in flood frequency estimation", Environment Agency (2017, ISBN: 978 1 84911 387 8). "Improving the FEH statistical procedures for flood frequency estimation", Environment Agency (2008, ISBN: 978 1 84432 920 5). "Low flow estimation in the United Kingdom", Institute of Hydrology (1992, ISBN 0 948540 45 1). Wallingford HydroSolutions, (2016, <http://software.hydrosolutions.co.uk/winfap4/Urban-Adjustment-Procedure-Technical-Note.pdf>). Data from the UK National River Flow Archive (<https://nrfa.ceh.ac.uk/>, terms and conditions: <https://nrfa.ceh.ac.uk/costs-terms-and-conditions>.
Author: Anthony Hammond
Maintainer: Anthony Hammond <agqhammond@gmail.com>
Diff between UKFE versions 0.1.0 dated 2020-11-23 and 0.1.1 dated 2020-11-24
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- R/All.R | 26 +++++++++++++------------- man/AMextract.Rd | 2 +- man/DesHydro.Rd | 2 +- man/EncProb.Rd | 4 ++-- man/HydroPlot.Rd | 2 +- man/ImportCDs.Rd | 6 +++--- man/POTextract.Rd | 2 +- man/TrendTest.Rd | 2 +- man/Uncertainty.Rd | 2 +- 11 files changed, 37 insertions(+), 37 deletions(-)
Title: Scatterplots with More Points
Description: C-based conversion of large scatterplot data to rasters. Speeds up
plotting of data with millions of points.
Author: Mirek Kratochvil [aut, cre] (<https://orcid.org/0000-0001-7356-4075>)
Maintainer: Mirek Kratochvil <exa.exa@gmail.com>
Diff between scattermore versions 0.6 dated 2020-03-06 and 0.7 dated 2020-11-24
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 15 +++++++++++++++ R/scattermore.R | 39 ++++++++++++++++++++++++++++++--------- man/geom_scattermore.Rd | 19 ++++++++++++++----- man/geom_scattermost.Rd | 11 ++++++++--- man/scattermore.Rd | 12 +++++++++--- man/scattermoreplot.Rd | 19 ++++++++++++++++--- src/scattermore.c | 8 ++++---- 9 files changed, 109 insertions(+), 40 deletions(-)
Title: Microbial Community Ecology Data Analysis
Description: A series of statistical and plotting approaches in microbial community ecology based on the R6 class. The classes are designed for data preprocessing, taxa abundance plotting, alpha diversity statistics, beta diversity statistics, differential abundance test and indicator taxon analysis, environmental data analysis, null model analysis, network analysis and functional analysis.
Author: Chi Liu [aut, cre],
Minjie Yao [aut],
Xiangzhen Li [aut],
Paul J. McMurdie [ctb],
Yang Cao [ctb],
James Robert White [ctb],
Stilianos Louca [cph],
Nhu H. Nguyen [cph]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between microeco versions 0.3.0 dated 2020-11-15 and 0.3.1 dated 2020-11-24
DESCRIPTION | 14 +++--- MD5 | 46 +++++++++++----------- R/microtable.R | 21 +++------- R/trans_abund.R | 23 +++++++---- R/trans_alpha.R | 9 +++- R/trans_beta.R | 4 + R/trans_diff.R | 4 - R/trans_func.R | 8 --- R/trans_network.R | 41 -------------------- R/trans_nullmodel.R | 4 + R/trans_venn.R | 4 + data/fungi_func.RData |binary data/otu_table_16S.RData |binary data/taxonomy_table_16S.RData |binary inst/CITATION | 2 man/microtable.Rd | 80 +++++++++------------------------------ man/trans_abund.Rd | 44 +++++++++++++++------ man/trans_alpha.Rd | 22 +++++++--- man/trans_beta.Rd | 12 ++++- man/trans_diff.Rd | 8 +-- man/trans_func.Rd | 36 ----------------- man/trans_network.Rd | 86 ------------------------------------------ man/trans_nullmodel.Rd | 12 ++++- man/trans_venn.Rd | 12 ++++- 24 files changed, 177 insertions(+), 315 deletions(-)
Title: Maximum Likelihood Estimation and Related Tools
Description: Functions for Maximum Likelihood (ML) estimation, non-linear
optimization, and related tools. It includes a unified way to call
different optimizers, and classes and methods to handle the results from
the Maximum Likelihood viewpoint. It also includes a number of convenience tools for testing
and developing your own models.
Author: Ott Toomet <otoomet@gmail.com>,
Arne Henningsen <arne.henningsen@gmail.com>,
with contributions from Spencer Graves and Yves Croissant
Maintainer: Ott Toomet <otoomet@gmail.com>
Diff between maxLik versions 1.4-4 dated 2020-09-04 and 1.4-6 dated 2020-11-24
maxLik-1.4-4/maxLik/R/head....R |only maxLik-1.4-6/maxLik/DESCRIPTION | 8 maxLik-1.4-6/maxLik/MD5 | 53 ++--- maxLik-1.4-6/maxLik/NEWS | 13 + maxLik-1.4-6/maxLik/R/10-MaxControl_class.R | 16 - maxLik-1.4-6/maxLik/R/compareDerivatives.R | 12 - maxLik-1.4-6/maxLik/R/headDots.R |only maxLik-1.4-6/maxLik/R/maxBFGSRCompute.R | 2 maxLik-1.4-6/maxLik/R/maxNRCompute.R | 30 -- maxLik-1.4-6/maxLik/R/maxSGACompute.R | 4 maxLik-1.4-6/maxLik/R/maximMessage.R | 10 maxLik-1.4-6/maxLik/R/returnCode.R | 7 maxLik-1.4-6/maxLik/build/vignette.rds |binary maxLik-1.4-6/maxLik/inst/doc/stochastic-gradient-maxLik.Rnw | 2 maxLik-1.4-6/maxLik/inst/doc/stochastic-gradient-maxLik.pdf |binary maxLik-1.4-6/maxLik/man/activePar.Rd | 24 +- maxLik-1.4-6/maxLik/man/compareDerivatives.Rd | 18 + maxLik-1.4-6/maxLik/man/maxLik-methods.Rd | 13 - maxLik-1.4-6/maxLik/man/maxLik-package.Rd | 77 +++---- maxLik-1.4-6/maxLik/man/maxLik.Rd | 65 ++++-- maxLik-1.4-6/maxLik/man/maxNR.Rd | 47 ++-- maxLik-1.4-6/maxLik/man/returnCode.Rd | 2 maxLik-1.4-6/maxLik/tests/finalHessian.Rout.save | 32 +-- maxLik-1.4-6/maxLik/tests/fitNormalDist_privateTest.Rout.save | 105 +++++----- maxLik-1.4-6/maxLik/tests/maxControl_privateTest.Rout.save | 6 maxLik-1.4-6/maxLik/tests/maxSG_privateTest.Rout.save | 6 maxLik-1.4-6/maxLik/tests/parameters_privateTest.Rout.save | 75 +------ maxLik-1.4-6/maxLik/vignettes/auto |only maxLik-1.4-6/maxLik/vignettes/stochastic-gradient-maxLik.Rnw | 2 29 files changed, 318 insertions(+), 311 deletions(-)
Title: Karl Broman's R Code
Description: Miscellaneous R functions, including functions related to
graphics (mostly for base graphics), permutation tests, running
mean/median, and general utilities.
Author: Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>),
Aimee Teo Broman [ctb] (<https://orcid.org/0000-0003-3783-2807>)
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between broman versions 0.70-4 dated 2020-05-22 and 0.71-6 dated 2020-11-24
DESCRIPTION | 10 ++++----- MD5 | 52 +++++++++++++++++++++++++-------------------------- NAMESPACE | 1 NEWS | 26 ++++++++++++++++++++++++- R/brocolors.R | 2 - R/ciplot.R | 8 ++++--- R/dotplot.R | 46 +++++++++++++++++++++++++++------------------ R/excel_fig.R | 2 - R/grayplot.R | 15 +++++--------- R/grayplot_na.R | 4 +-- R/holmans_triangle.R | 4 +-- R/jiggle.R | 13 ++++++++++-- R/mypairs.R | 2 - man/dotplot.Rd | 6 +++-- man/grayplot.Rd | 4 +-- man/grayplot_na.Rd | 2 - man/jiggle.Rd | 12 ++++++++++- man/mypairs.Rd | 2 - man/myround.Rd | 2 - man/objectsizes.Rd | 2 - man/paste..Rd | 2 - man/paste00.Rd | 2 - man/qqline2.Rd | 6 ++--- man/revrainbow.Rd | 6 ++--- man/rmvn.Rd | 2 - man/triplot.Rd | 2 - man/twocolorpal.Rd | 2 - 27 files changed, 145 insertions(+), 92 deletions(-)
Title: Taxonomic Uncertainty on Multivariate Analyses of Ecological
Data
Description: Permutational method to incorporate taxonomic uncertainty and some functions to assess its effects on parameters of some widely used multivariate methods in ecology, as explained in Cayuela et al. (2011) <doi:10.1111/j.1600-0587.2009.05899.x>.
Author: Luis Cayuela and Marcelino de la Cruz
Maintainer: Luis Cayuela <luis.cayuela@urjc.es>
Diff between betaper versions 1.1-1 dated 2020-03-02 and 1.1-2 dated 2020-11-24
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- R/pertables.p2.R | 3 ++- man/adonis_pertables.Rd | 5 ++--- man/cca_pertables.Rd | 5 ++--- man/mantel_pertables.Rd | 5 ++--- man/pertables.Rd | 8 +++++--- man/rda_pertables.Rd | 5 ++--- 9 files changed, 28 insertions(+), 29 deletions(-)
Title: Extracts Sentiment and Sentiment-Derived Plot Arcs from Text
Description: Extracts sentiment and sentiment-derived plot arcs
from text using a variety of sentiment dictionaries conveniently
packaged for consumption by R users. Implemented dictionaries include
"syuzhet" (default) developed in the Nebraska Literary Lab
"afinn" developed by Finn Årup Nielsen, "bing" developed by Minqing Hu
and Bing Liu, and "nrc" developed by Mohammad, Saif M. and Turney, Peter D.
Applicable references are available in README.md and in the documentation
for the "get_sentiment" function. The package also provides a hack for
implementing Stanford's coreNLP sentiment parser. The package provides
several methods for plot arc normalization.
Author: Matthew Jockers [aut, cre]
Maintainer: Matthew Jockers <mjockers@gmail.com>
Diff between syuzhet versions 1.0.4 dated 2017-12-14 and 1.0.6 dated 2020-11-24
DESCRIPTION | 21 MD5 | 37 - NAMESPACE | 2 R/sysdata.rda |binary R/syuzhet.R | 119 ++++- README.md | 2 build/vignette.rds |binary inst/doc/syuzhet-vignette.R | 102 ++-- inst/doc/syuzhet-vignette.Rmd | 65 ++- inst/doc/syuzhet-vignette.html | 854 ++++++++++++++++++++++++++-------------- inst/extdata/quijote.txt | 573 -------------------------- man/get_dct_transform.Rd | 9 man/get_nrc_sentiment.Rd | 4 man/get_sentiment.Rd | 18 man/get_sentiment_dictionary.Rd | 6 man/get_tokens.Rd | 4 man/get_transformed_values.Rd | 10 man/mixed_messages.Rd |only man/simple_plot.Rd | 9 vignettes/syuzhet-vignette.Rmd | 65 ++- 20 files changed, 907 insertions(+), 993 deletions(-)
Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models with and without asymmetry (leverage) via Markov chain Monte Carlo (MCMC) methods. Methodological details are given in Kastner and Frühwirth-Schnatter (2014) <doi:10.1016/j.csda.2013.01.002> and Hosszejni and Kastner (2019) <doi:10.1007/978-3-030-30611-3_8>; the most common use cases are described in Kastner (2016) <doi:10.18637/jss.v069.i05> and the package vignette.
Author: Darjus Hosszejni [aut, cre] (<https://orcid.org/0000-0002-3803-691X>),
Gregor Kastner [aut] (<https://orcid.org/0000-0002-8237-8271>)
Maintainer: Darjus Hosszejni <darjus.hosszejni@wu.ac.at>
Diff between stochvol versions 3.0.2 dated 2020-11-17 and 3.0.3 dated 2020-11-24
DESCRIPTION | 9 ++++----- MD5 | 34 +++++++++++++++++----------------- NEWS | 3 +++ R/util.R | 8 ++++---- R/wrappers.R | 8 ++++---- inst/doc/article2.R | 12 +++--------- inst/doc/article2.Rnw | 35 +++++++++++++++-------------------- inst/doc/article2.pdf |binary inst/examples/svsample.R | 4 ++-- inst/include/stochvol.h | 2 +- man/svsample.Rd | 4 ++-- src/sampling_latent_states.cc | 6 +++--- src/sampling_main.cc | 16 ++++++++-------- src/utils_main.h | 3 +++ tests/testthat/test-samplers.R | 9 +++------ tests/testthat/test-wrappers.R | 4 ++++ vignettes/article2.Rnw | 35 +++++++++++++++-------------------- vignettes/ref.bib | 9 ++++++++- 18 files changed, 99 insertions(+), 102 deletions(-)
More information about SpatialRegimes at CRAN
Permanent link
Title: Robust Bootstrap Forecast Densities for GARCH Models
Description: Bootstrap forecast densities for GARCH (Generalized Autoregressive Conditional Heteroskedastic) returns and volatilities using the robust residual-based bootstrap procedure of Trucios, Hotta and Ruiz (2017) <DOI:10.1080/00949655.2017.1359601>.
Author: Carlos Trucios
Maintainer: Carlos Trucios <ctrucios@gmail.com>
Diff between RobGARCHBoot versions 1.0.1 dated 2020-05-13 and 1.1.0 dated 2020-11-24
DESCRIPTION | 14 +++++++------- MD5 | 25 ++++++++++++++----------- NAMESPACE | 8 ++++++++ R/ROBUSTGARCH.R | 6 ++---- R/RcppExports.R | 1 + R/RobGARCHBoot.R | 17 +++++++++++++---- R/RobGARCHBootParallel.R |only R/bootstrap_replication.R |only README.md | 9 +++++++-- man/ROBUSTGARCH.Rd | 3 +-- man/RobGARCHBoot-package.Rd | 11 ++++++----- man/RobGARCHBoot.Rd | 9 ++++++--- man/RobGARCHBootParallel.Rd |only man/fitted_Vol.Rd | 2 +- src/ROBUSTGARCH.cpp | 2 +- 15 files changed, 67 insertions(+), 40 deletions(-)
Title: Junction Tree Inference
Description: Minimal and memory efficient implementation of the junction tree
algorithm using the Lauritzen-Spiegelhalter scheme;
S. L. Lauritzen and D. J. Spiegelhalter (1988)
<https://www.jstor.org/stable/2345762?seq=1>.
Author: Mads Lindskou [aut, cre]
Maintainer: Mads Lindskou <mads@math.aau.dk>
Diff between jti versions 0.5.1 dated 2020-11-19 and 0.5.2 dated 2020-11-24
DESCRIPTION | 8 ++-- MD5 | 12 +++---- NEWS.md | 4 ++ R/api_compile.R | 2 - R/helper_charge.R | 2 - R/helper_jt.R | 91 +++++++++++++++++++++++++----------------------------- R/sandbox.R | 59 ++++++++++++++++++++++++----------- 7 files changed, 100 insertions(+), 78 deletions(-)
Title: Kaplan-Meier Plot with 'ggplot2'
Description: The function 'jskm()' creates publication quality Kaplan-Meier plot with at risk tables below. 'svyjskm()' provides plot for weighted Kaplan-Meier estimator.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jskm versions 0.4.1 dated 2020-11-01 and 0.4.2 dated 2020-11-24
DESCRIPTION | 8 - MD5 | 40 ++++----- NEWS.md | 4 R/jskm.R | 26 +++++- R/svyjskm.R | 20 ++++ README.md | 14 ++- build/vignette.rds |binary inst/doc/jskm.R | 10 +- inst/doc/jskm.Rmd | 12 +- inst/doc/jskm.html | 130 ++++++++++++------------------- man/figures/README-unnamed-chunk-1-2.png |binary man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-3-2.png |binary man/figures/README-unnamed-chunk-4-2.png |binary man/figures/README-unnamed-chunk-4-3.png |binary man/figures/README-unnamed-chunk-5-3.png |binary man/jskm.Rd | 5 - man/svyjskm.Rd | 5 - tests/testthat/test-km.R | 10 +- vignettes/jskm.Rmd | 12 +- 21 files changed, 162 insertions(+), 134 deletions(-)
Title: Correlations in R
Description: A tool for exploring correlations.
It makes it possible to easily perform routine tasks when
exploring correlation matrices such as ignoring the diagonal,
focusing on the correlations of certain variables against others,
or rearranging and visualizing the matrix in terms of the
strength of the correlations.
Author: Max Kuhn [aut, cre],
Simon Jackson [aut],
Jorge Cimentada [aut]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between corrr versions 0.4.2 dated 2020-03-22 and 0.4.3 dated 2020-11-24
corrr-0.4.2/corrr/tests/testthat/stretch.txt |only corrr-0.4.2/corrr/tools |only corrr-0.4.3/corrr/DESCRIPTION | 19 - corrr-0.4.3/corrr/MD5 | 94 ++++---- corrr-0.4.3/corrr/NAMESPACE | 2 corrr-0.4.3/corrr/NEWS.md | 21 + corrr-0.4.3/corrr/R/colpair.R |only corrr-0.4.3/corrr/R/cor_df.R | 172 +++++++++------ corrr-0.4.3/corrr/R/correlate.R | 77 +++--- corrr-0.4.3/corrr/R/dataframe.R | 4 corrr-0.4.3/corrr/R/internal.R | 12 - corrr-0.4.3/corrr/R/matrix.R | 4 corrr-0.4.3/corrr/R/output.R | 74 +++--- corrr-0.4.3/corrr/R/reshape.R | 56 ++--- corrr-0.4.3/corrr/R/utility.R | 48 ++-- corrr-0.4.3/corrr/README.md | 73 +++--- corrr-0.4.3/corrr/build/vignette.rds |binary corrr-0.4.3/corrr/inst/doc/databases.Rmd | 2 corrr-0.4.3/corrr/inst/doc/databases.html | 96 +++++++- corrr-0.4.3/corrr/inst/doc/using-corrr.R | 8 corrr-0.4.3/corrr/inst/doc/using-corrr.Rmd | 12 - corrr-0.4.3/corrr/inst/doc/using-corrr.html | 188 +++++++++++------ corrr-0.4.3/corrr/man/as_cordf.Rd | 2 corrr-0.4.3/corrr/man/as_matrix.Rd | 2 corrr-0.4.3/corrr/man/colpair_map.Rd |only corrr-0.4.3/corrr/man/correlate.Rd | 25 +- corrr-0.4.3/corrr/man/corrr-package.Rd | 1 corrr-0.4.3/corrr/man/fashion.Rd | 2 corrr-0.4.3/corrr/man/figures/README-combination-1.png |only corrr-0.4.3/corrr/man/figures/README-combination-2.png |only corrr-0.4.3/corrr/man/figures/logo.png |binary corrr-0.4.3/corrr/man/figures/to-cor-df.png |only corrr-0.4.3/corrr/man/first_col.Rd | 6 corrr-0.4.3/corrr/man/focus.Rd | 8 corrr-0.4.3/corrr/man/network_plot.Rd | 5 corrr-0.4.3/corrr/man/rplot.Rd | 20 + corrr-0.4.3/corrr/man/stretch.Rd | 4 corrr-0.4.3/corrr/tests/testthat/test-as_cordf.R | 16 - corrr-0.4.3/corrr/tests/testthat/test-as_matrix.R | 56 ++--- corrr-0.4.3/corrr/tests/testthat/test-colpair.R |only corrr-0.4.3/corrr/tests/testthat/test-correlate.R | 15 + corrr-0.4.3/corrr/tests/testthat/test-dataframe.R | 2 corrr-0.4.3/corrr/tests/testthat/test-fashion.R | 2 corrr-0.4.3/corrr/tests/testthat/test-focus.R | 18 - corrr-0.4.3/corrr/tests/testthat/test-focus_.R | 14 - corrr-0.4.3/corrr/tests/testthat/test-plots.R | 28 +- corrr-0.4.3/corrr/tests/testthat/test-rearrange.R | 2 corrr-0.4.3/corrr/tests/testthat/test-stretch.R | 29 ++ corrr-0.4.3/corrr/tests/testthat/test-utilities.R | 6 corrr-0.4.3/corrr/vignettes/databases.Rmd | 2 corrr-0.4.3/corrr/vignettes/using-corrr.Rmd | 12 - 51 files changed, 762 insertions(+), 477 deletions(-)
Title: Hidden Markov Models of Character Evolution
Description: Fits hidden Markov models of discrete character evolution which allow different transition rate classes on different portions of a phylogeny. Beaulieu et al (2013) <doi:10.1093/sysbio/syt034>.
Author: Jeremy Beaulieu [aut, cre],
Brian O'Meara [aut],
Jeffrey Oliver [aut],
James Boyko [aut]
Maintainer: Jeremy Beaulieu <jmbeauli@uark.edu>
Diff between corHMM versions 2.4 dated 2020-10-01 and 2.5 dated 2020-11-24
DESCRIPTION | 8 MD5 | 31 +-- R/ancRECON.R | 176 +++++++++++++++++++ R/corHMM.R | 4 R/makeSimmap.R | 330 ++++++++++++++++++++++--------------- R/rate.mat.maker.R | 15 - R/rayDISC.R | 4 inst/doc/corHMMv2.1-vignette.R | 23 +- inst/doc/corHMMv2.1-vignette.Rmd | 24 +- inst/doc/corHMMv2.1-vignette.pdf |binary man/ancRECON.Rd | 4 man/corHMM.Rd | 6 man/makeSimmap.Rd | 20 -- man/rayDISC.Rd | 4 vignettes/corHMMResults.Rsave |only vignettes/corHMMv2.1-vignette.Rmd | 24 +- vignettes/corHMMv2.1-vignette.html | 262 ++++++++++------------------- 17 files changed, 539 insertions(+), 396 deletions(-)
Title: Versatile Curation of Table Metadata
Description: A file-based
mechanism for documenting datasets. It reads and writes
YAML-formatted metadata and applies it as data
item attributes. Data and metadata are stored independently
but can be coordinated by using similar file paths with
different extensions. The 'yamlet' dialect is valid 'YAML',
but some conventions are chosen to improve readability.
Defaults and conventions can be over-ridden by the user.
See ?yamlet and ?decorate.data.frame.
See ?read_yamlet ?write_yamlet, and ?io_csv.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between yamlet versions 0.4.8 dated 2020-06-18 and 0.5.1 dated 2020-11-24
yamlet-0.4.8/yamlet/R/agplot.R |only yamlet-0.4.8/yamlet/man/print.decorated.Rd |only yamlet-0.4.8/yamlet/man/print.dg.Rd |only yamlet-0.4.8/yamlet/man/resolve.data.frame.Rd |only yamlet-0.5.1/yamlet/DESCRIPTION | 12 yamlet-0.5.1/yamlet/MD5 | 273 +++++----- yamlet-0.5.1/yamlet/NAMESPACE | 29 + yamlet-0.5.1/yamlet/R/alias.R | 21 yamlet-0.5.1/yamlet/R/append_units.R | 26 - yamlet-0.5.1/yamlet/R/classified.R | 2 yamlet-0.5.1/yamlet/R/conditionalize.R | 2 yamlet-0.5.1/yamlet/R/decorate.R |only yamlet-0.5.1/yamlet/R/explicit_guide.R | 52 +- yamlet-0.5.1/yamlet/R/factorize_codelist.R | 12 yamlet-0.5.1/yamlet/R/ggplot.R |only yamlet-0.5.1/yamlet/R/ggplot_ggready.R |only yamlet-0.5.1/yamlet/R/ggready.R | 143 ++++- yamlet-0.5.1/yamlet/R/io_res.R |only yamlet-0.5.1/yamlet/R/modify.R |only yamlet-0.5.1/yamlet/R/named.R |only yamlet-0.5.1/yamlet/R/parseable.R | 1 yamlet-0.5.1/yamlet/R/resolve.R | 18 yamlet-0.5.1/yamlet/R/selected.R |only yamlet-0.5.1/yamlet/R/singularity.R |only yamlet-0.5.1/yamlet/R/sub_units.R | 11 yamlet-0.5.1/yamlet/R/xtable.R | 63 +- yamlet-0.5.1/yamlet/R/yamlet.R | 376 +-------------- yamlet-0.5.1/yamlet/build/vignette.rds |binary yamlet-0.5.1/yamlet/inst/doc/yamlet-introduction.R | 4 yamlet-0.5.1/yamlet/inst/doc/yamlet-introduction.Rmd | 4 yamlet-0.5.1/yamlet/inst/doc/yamlet-introduction.html | 363 ++++++++------ yamlet-0.5.1/yamlet/man/alias.data.frame.Rd | 79 +-- yamlet-0.5.1/yamlet/man/anti_join.decorated.Rd | 128 ++--- yamlet-0.5.1/yamlet/man/append_units.Rd | 73 +- yamlet-0.5.1/yamlet/man/append_units.data.frame.Rd | 73 +- yamlet-0.5.1/yamlet/man/append_units.default.Rd | 124 ++-- yamlet-0.5.1/yamlet/man/arrange.decorated.Rd | 76 +-- yamlet-0.5.1/yamlet/man/as.character.yam.Rd | 82 +-- yamlet-0.5.1/yamlet/man/as.character.yamlet.Rd | 89 +-- yamlet-0.5.1/yamlet/man/as_classified.Rd | 60 +- yamlet-0.5.1/yamlet/man/as_classified.factor.Rd | 77 +-- yamlet-0.5.1/yamlet/man/as_decorated.Rd | 93 ++- yamlet-0.5.1/yamlet/man/as_decorated.default.Rd |only yamlet-0.5.1/yamlet/man/as_spork.symbolic_units.Rd | 86 +-- yamlet-0.5.1/yamlet/man/as_spork.unit_string.Rd | 70 +- yamlet-0.5.1/yamlet/man/as_spork.units.Rd | 72 +- yamlet-0.5.1/yamlet/man/as_unit_string.Rd | 76 +-- yamlet-0.5.1/yamlet/man/as_unit_string.character.Rd | 68 +- yamlet-0.5.1/yamlet/man/as_unit_string.factor.Rd | 70 +- yamlet-0.5.1/yamlet/man/as_unit_string.symbolic_units.Rd | 94 +-- yamlet-0.5.1/yamlet/man/as_unit_string.units.Rd | 76 +-- yamlet-0.5.1/yamlet/man/as_yam.Rd | 56 +- yamlet-0.5.1/yamlet/man/as_yam.character.Rd | 90 +-- yamlet-0.5.1/yamlet/man/as_yam.yamlet.Rd | 90 +-- yamlet-0.5.1/yamlet/man/as_yamlet.Rd | 74 +- yamlet-0.5.1/yamlet/man/as_yamlet.character.Rd | 116 ++-- yamlet-0.5.1/yamlet/man/as_yamlet.data.frame.Rd | 67 +- yamlet-0.5.1/yamlet/man/as_yamlet.list.Rd |only yamlet-0.5.1/yamlet/man/as_yamlet.yam.Rd | 82 +-- yamlet-0.5.1/yamlet/man/as_yamlet.yamlet.Rd | 65 +- yamlet-0.5.1/yamlet/man/conditionalize.Rd | 58 +- yamlet-0.5.1/yamlet/man/conditionalize.data.frame.Rd | 163 ++---- yamlet-0.5.1/yamlet/man/decorate.Rd | 83 +-- yamlet-0.5.1/yamlet/man/decorate.character.Rd | 226 ++++----- yamlet-0.5.1/yamlet/man/decorate.data.frame.Rd | 140 ++--- yamlet-0.5.1/yamlet/man/decorate.list.Rd | 100 ++- yamlet-0.5.1/yamlet/man/decorations.Rd | 77 +-- yamlet-0.5.1/yamlet/man/decorations.data.frame.Rd | 114 ++-- yamlet-0.5.1/yamlet/man/encode.yamlet.Rd | 71 +- yamlet-0.5.1/yamlet/man/explicit_guide.Rd | 59 +- yamlet-0.5.1/yamlet/man/explicit_guide.data.frame.Rd | 118 ++-- yamlet-0.5.1/yamlet/man/explicit_guide.yamlet.Rd | 124 ++-- yamlet-0.5.1/yamlet/man/factorize_codelist.Rd | 61 +- yamlet-0.5.1/yamlet/man/factorize_codelist.character.Rd | 66 +- yamlet-0.5.1/yamlet/man/factorize_codelist.data.frame.Rd | 71 +- yamlet-0.5.1/yamlet/man/factorize_codelist.default.Rd | 56 +- yamlet-0.5.1/yamlet/man/factorize_codelist.factor.Rd | 58 +- yamlet-0.5.1/yamlet/man/filter.decorated.Rd | 123 +++- yamlet-0.5.1/yamlet/man/footnote.decorated.Rd | 89 +-- yamlet-0.5.1/yamlet/man/full_join.decorated.Rd | 136 ++--- yamlet-0.5.1/yamlet/man/ggplot.decorated.Rd | 199 +++++-- yamlet-0.5.1/yamlet/man/ggplot.ggready.Rd |only yamlet-0.5.1/yamlet/man/ggplot_build.decorated_ggplot.Rd |only yamlet-0.5.1/yamlet/man/ggplot_build.ggready_ggplot.Rd |only yamlet-0.5.1/yamlet/man/ggready.Rd | 101 ++-- yamlet-0.5.1/yamlet/man/ggready.data.frame.Rd | 104 +--- yamlet-0.5.1/yamlet/man/ggready.decorated.Rd |only yamlet-0.5.1/yamlet/man/ggready.resolved.Rd |only yamlet-0.5.1/yamlet/man/group_by.decorated.Rd | 99 +-- yamlet-0.5.1/yamlet/man/inner_join.decorated.Rd | 136 ++--- yamlet-0.5.1/yamlet/man/io_csv.Rd | 90 +-- yamlet-0.5.1/yamlet/man/io_csv.character.Rd | 121 ++-- yamlet-0.5.1/yamlet/man/io_csv.data.frame.Rd | 157 +++--- yamlet-0.5.1/yamlet/man/io_res.Rd |only yamlet-0.5.1/yamlet/man/io_res.character.Rd |only yamlet-0.5.1/yamlet/man/io_table.Rd | 92 +-- yamlet-0.5.1/yamlet/man/io_table.character.Rd | 121 ++-- yamlet-0.5.1/yamlet/man/io_table.data.frame.Rd | 155 +++--- yamlet-0.5.1/yamlet/man/io_yamlet.Rd | 90 +-- yamlet-0.5.1/yamlet/man/io_yamlet.character.Rd | 131 ++--- yamlet-0.5.1/yamlet/man/io_yamlet.data.frame.Rd | 163 +++--- yamlet-0.5.1/yamlet/man/io_yamlet.yamlet.Rd | 126 ++--- yamlet-0.5.1/yamlet/man/isConditional.default.Rd | 52 +- yamlet-0.5.1/yamlet/man/isConditional.list.Rd | 64 +- yamlet-0.5.1/yamlet/man/isLevels.character.Rd | 62 +- yamlet-0.5.1/yamlet/man/isLevels.default.Rd | 52 +- yamlet-0.5.1/yamlet/man/is_parseable.Rd | 58 +- yamlet-0.5.1/yamlet/man/is_parseable.default.Rd | 110 ++-- yamlet-0.5.1/yamlet/man/left_join.decorated.Rd | 136 ++--- yamlet-0.5.1/yamlet/man/list2encoding.Rd | 64 +- yamlet-0.5.1/yamlet/man/modify.Rd |only yamlet-0.5.1/yamlet/man/modify.default.Rd |only yamlet-0.5.1/yamlet/man/mutate.decorated.Rd | 94 +-- yamlet-0.5.1/yamlet/man/named.Rd |only yamlet-0.5.1/yamlet/man/print.decorated_ggplot.Rd |only yamlet-0.5.1/yamlet/man/print.decorated_xtable.Rd |only yamlet-0.5.1/yamlet/man/print.decorations.Rd |only yamlet-0.5.1/yamlet/man/print.ggready_ggplot.Rd |only yamlet-0.5.1/yamlet/man/print.yamlet.Rd | 60 +- yamlet-0.5.1/yamlet/man/promote.Rd |only yamlet-0.5.1/yamlet/man/promote.default.Rd |only yamlet-0.5.1/yamlet/man/read_yamlet.Rd | 115 ++-- yamlet-0.5.1/yamlet/man/redecorate.Rd | 89 +-- yamlet-0.5.1/yamlet/man/reexports.Rd | 48 - yamlet-0.5.1/yamlet/man/resolve.Rd | 60 +- yamlet-0.5.1/yamlet/man/resolve.decorated.Rd |only yamlet-0.5.1/yamlet/man/right_join.decorated.Rd | 136 ++--- yamlet-0.5.1/yamlet/man/select.decorated.Rd | 80 +-- yamlet-0.5.1/yamlet/man/selected.Rd |only yamlet-0.5.1/yamlet/man/selected.default.Rd |only yamlet-0.5.1/yamlet/man/semi_join.decorated.Rd | 128 ++--- yamlet-0.5.1/yamlet/man/singularity.Rd | 117 ++-- yamlet-0.5.1/yamlet/man/slice.decorated.Rd | 96 +-- yamlet-0.5.1/yamlet/man/sub-.classified.Rd | 64 +- yamlet-0.5.1/yamlet/man/sub-.decorated.Rd |only yamlet-0.5.1/yamlet/man/sub-.unit_string.Rd | 80 +-- yamlet-0.5.1/yamlet/man/sub-.yamlet.Rd | 67 +- yamlet-0.5.1/yamlet/man/sub-sub-.unit_string.Rd | 80 +-- yamlet-0.5.1/yamlet/man/sub_units.Rd | 147 ++--- yamlet-0.5.1/yamlet/man/summarise.decorated.Rd | 90 +-- yamlet-0.5.1/yamlet/man/summarize.decorated.Rd | 90 +-- yamlet-0.5.1/yamlet/man/to_yamlet.NULL.Rd | 62 +- yamlet-0.5.1/yamlet/man/to_yamlet.Rd | 60 +- yamlet-0.5.1/yamlet/man/to_yamlet.character.Rd | 68 +- yamlet-0.5.1/yamlet/man/to_yamlet.default.Rd | 68 +- yamlet-0.5.1/yamlet/man/to_yamlet.list.Rd | 66 +- yamlet-0.5.1/yamlet/man/unnest.Rd | 72 +- yamlet-0.5.1/yamlet/man/unnest.default.Rd | 54 +- yamlet-0.5.1/yamlet/man/unnest.list.Rd | 76 +-- yamlet-0.5.1/yamlet/man/write_yamlet.Rd | 143 ++--- yamlet-0.5.1/yamlet/man/xtable.decorated.Rd | 80 +-- yamlet-0.5.1/yamlet/man/yamlet.Rd | 192 +++---- yamlet-0.5.1/yamlet/tests/testthat/Rplots.pdf |only yamlet-0.5.1/yamlet/tests/testthat/test-yamlet.R | 349 +++++++++++++ yamlet-0.5.1/yamlet/vignettes/yamlet-introduction.Rmd | 4 155 files changed, 5757 insertions(+), 5272 deletions(-)
Title: Sparse Tables
Description: Fast Multiplication and Marginalization of Sparse Tables.
Author: Mads Lindskou [aut, cre]
Maintainer: Mads Lindskou <mads@math.aau.dk>
Diff between sparta versions 0.6.0 dated 2020-11-09 and 0.6.1 dated 2020-11-24
DESCRIPTION | 10 +-- MD5 | 20 +++--- NEWS.md | 4 + R/RcppExports.R | 8 +- R/api_sparta.R | 12 +-- R/helpers_sparta.R | 52 ++++++++++------- R/sparta-package.R | 2 README.md | 1 man/sparta-package.Rd | 2 src/RcppExports.cpp | 26 ++++++-- src/marginalize.cpp | 152 +++++++++++++++++++++++++++++++++++++++++++------- 11 files changed, 218 insertions(+), 71 deletions(-)
Title: Media News Extraction for Text Analysis
Description: Extract textual data from different media channels
through its source, based on users choice of keywords.
These data can be used to perform text analysis to
identify patterns in respective media reporting.
The media channels used in this package are print media
from India. The data (or news) used are publicly
available to consumers.
Author: Vatsal Aima
Maintainer: Vatsal Aima <vaima75@hotmail.com>
Diff between MediaNews versions 0.1.0 dated 2020-02-09 and 0.2.0 dated 2020-11-24
DESCRIPTION | 14 +++++------ MD5 | 14 +++++------ NAMESPACE | 3 -- R/ClearText.R | 2 - R/TOI_News_Articles.R | 55 ++++++++++++++++++++++++----------------------- R/TOI_News_Dataset.R | 10 +++----- README.md | 7 ++--- man/TOI_News_Articles.Rd | 21 +++++------------ 8 files changed, 59 insertions(+), 67 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent access to
information contained in various R models, like model formulas, model terms,
information about random effects, data that was used to fit the model or
data from response variables. 'insight' mainly revolves around two types
of functions: Functions that find (the names of) information, starting with
'find_', and functions that get the underlying data, starting with 'get_'.
The package has a consistent syntax and works with many different model
objects, where otherwise functions to access these information are missing.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>),
Indrajeet Patil [aut, ctb] (<https://orcid.org/0000-0003-1995-6531>),
Philip Waggoner [aut, ctb] (<https://orcid.org/0000-0002-7825-7573>),
Mattan S. Ben-Shachar [aut, ctb]
(<https://orcid.org/0000-0002-4287-4801>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between insight versions 0.10.0 dated 2020-10-22 and 0.11.0 dated 2020-11-24
insight-0.10.0/insight/man/format_table.Rd |only insight-0.11.0/insight/DESCRIPTION | 15 insight-0.11.0/insight/MD5 | 272 ++--- insight-0.11.0/insight/NAMESPACE | 49 + insight-0.11.0/insight/NEWS.md | 480 ++++++++-- insight-0.11.0/insight/R/clean_parameters.R | 10 insight-0.11.0/insight/R/colour_tools.R | 5 insight-0.11.0/insight/R/display.R |only insight-0.11.0/insight/R/export_table.R |only insight-0.11.0/insight/R/find_algorithm.R | 3 insight-0.11.0/insight/R/find_formula.R | 113 +- insight-0.11.0/insight/R/find_offset.R |only insight-0.11.0/insight/R/find_parameters.R | 107 ++ insight-0.11.0/insight/R/find_response.R | 11 insight-0.11.0/insight/R/find_statistic.R | 19 insight-0.11.0/insight/R/find_terms.R | 7 insight-0.11.0/insight/R/find_variables.R | 49 - insight-0.11.0/insight/R/format_bf.R | 26 insight-0.11.0/insight/R/format_ci.R | 27 insight-0.11.0/insight/R/format_table.R | 448 ++++++++- insight-0.11.0/insight/R/format_value.R | 4 insight-0.11.0/insight/R/get_data.R | 70 + insight-0.11.0/insight/R/get_parameters.R | 158 ++- insight-0.11.0/insight/R/get_priors.R | 68 + insight-0.11.0/insight/R/get_response.R | 4 insight-0.11.0/insight/R/get_statistic.R | 20 insight-0.11.0/insight/R/get_varcov.R | 7 insight-0.11.0/insight/R/get_variances.R | 36 insight-0.11.0/insight/R/helper_functions.R | 193 +++- insight-0.11.0/insight/R/is_model.R | 9 insight-0.11.0/insight/R/is_model_supported.R | 8 insight-0.11.0/insight/R/model_info.R | 15 insight-0.11.0/insight/R/n_obs.R | 12 insight-0.11.0/insight/R/null_model.R | 6 insight-0.11.0/insight/R/print_parameters.R | 60 + insight-0.11.0/insight/R/standardize_names.R | 164 ++- insight-0.11.0/insight/R/utils_get_data.R | 26 insight-0.11.0/insight/R/utils_model_info.R | 78 + insight-0.11.0/insight/README.md | 63 - insight-0.11.0/insight/build/partial.rdb |binary insight-0.11.0/insight/inst/WORDLIST | 65 - insight-0.11.0/insight/inst/doc/insight.html | 100 -- insight-0.11.0/insight/man/display.Rd |only insight-0.11.0/insight/man/export_table.Rd |only insight-0.11.0/insight/man/find_offset.Rd |only insight-0.11.0/insight/man/find_response.Rd | 3 insight-0.11.0/insight/man/find_terms.Rd | 2 insight-0.11.0/insight/man/find_variables.Rd | 49 - insight-0.11.0/insight/man/format_bf.Rd | 1 insight-0.11.0/insight/man/format_ci.Rd | 3 insight-0.11.0/insight/man/format_value.Rd | 127 +- insight-0.11.0/insight/man/get_parameters.Rd | 19 insight-0.11.0/insight/man/get_priors.Rd | 5 insight-0.11.0/insight/man/get_variance.Rd | 16 insight-0.11.0/insight/man/model_info.Rd | 6 insight-0.11.0/insight/man/parameters_table.Rd |only insight-0.11.0/insight/man/print_parameters.Rd | 15 insight-0.11.0/insight/man/standardize_names.Rd | 26 insight-0.11.0/insight/tests/spelling.R | 9 insight-0.11.0/insight/tests/testthat/test-BayesFactorBF.R | 85 + insight-0.11.0/insight/tests/testthat/test-GLMMadaptive.R | 4 insight-0.11.0/insight/tests/testthat/test-Gam2.R | 6 insight-0.11.0/insight/tests/testthat/test-LORgee.R | 6 insight-0.11.0/insight/tests/testthat/test-MCMCglmm.R | 20 insight-0.11.0/insight/tests/testthat/test-aovlist.R | 6 insight-0.11.0/insight/tests/testthat/test-backticks.R | 1 insight-0.11.0/insight/tests/testthat/test-betabin.R | 8 insight-0.11.0/insight/tests/testthat/test-betareg.R | 7 insight-0.11.0/insight/tests/testthat/test-bigglm.R | 5 insight-0.11.0/insight/tests/testthat/test-blmer.R | 10 insight-0.11.0/insight/tests/testthat/test-brms.R | 8 insight-0.11.0/insight/tests/testthat/test-censReg.R | 6 insight-0.11.0/insight/tests/testthat/test-cgam.R | 11 insight-0.11.0/insight/tests/testthat/test-clean_names.R | 1 insight-0.11.0/insight/tests/testthat/test-clm.R | 5 insight-0.11.0/insight/tests/testthat/test-clm2.R | 5 insight-0.11.0/insight/tests/testthat/test-clmm.R | 8 insight-0.11.0/insight/tests/testthat/test-coxme.R | 8 insight-0.11.0/insight/tests/testthat/test-coxph.R | 14 insight-0.11.0/insight/tests/testthat/test-cpglmm.R | 7 insight-0.11.0/insight/tests/testthat/test-crch.R | 6 insight-0.11.0/insight/tests/testthat/test-crq.R | 5 insight-0.11.0/insight/tests/testthat/test-data.frame.R | 2 insight-0.11.0/insight/tests/testthat/test-feis.R | 5 insight-0.11.0/insight/tests/testthat/test-felm.R | 3 insight-0.11.0/insight/tests/testthat/test-find_predictor_nested_re.R | 2 insight-0.11.0/insight/tests/testthat/test-fixest.R | 8 insight-0.11.0/insight/tests/testthat/test-format.R | 18 insight-0.11.0/insight/tests/testthat/test-gam.R | 9 insight-0.11.0/insight/tests/testthat/test-gamlss.R | 5 insight-0.11.0/insight/tests/testthat/test-gamm.R | 4 insight-0.11.0/insight/tests/testthat/test-gamm4.R | 3 insight-0.11.0/insight/tests/testthat/test-gbm.R | 3 insight-0.11.0/insight/tests/testthat/test-gee.R | 5 insight-0.11.0/insight/tests/testthat/test-geeglm.R | 5 insight-0.11.0/insight/tests/testthat/test-get_data.R | 11 insight-0.11.0/insight/tests/testthat/test-glm.R | 8 insight-0.11.0/insight/tests/testthat/test-glmmTMB.R | 10 insight-0.11.0/insight/tests/testthat/test-glmrob_base.R | 6 insight-0.11.0/insight/tests/testthat/test-gls.R | 3 insight-0.11.0/insight/tests/testthat/test-has_intercept.R | 2 insight-0.11.0/insight/tests/testthat/test-hurdle.R | 6 insight-0.11.0/insight/tests/testthat/test-is_nullmodel.R | 2 insight-0.11.0/insight/tests/testthat/test-iv_robust.R | 3 insight-0.11.0/insight/tests/testthat/test-ivreg.R | 39 insight-0.11.0/insight/tests/testthat/test-ivreg_AER.R |only insight-0.11.0/insight/tests/testthat/test-lm.R | 8 insight-0.11.0/insight/tests/testthat/test-lm_robust.R | 5 insight-0.11.0/insight/tests/testthat/test-lme.R | 8 insight-0.11.0/insight/tests/testthat/test-lmer.R | 26 insight-0.11.0/insight/tests/testthat/test-lmrob_base.R | 5 insight-0.11.0/insight/tests/testthat/test-logistf.R | 6 insight-0.11.0/insight/tests/testthat/test-mixed.R | 6 insight-0.11.0/insight/tests/testthat/test-mlogit.R | 1 insight-0.11.0/insight/tests/testthat/test-model_data.R | 2 insight-0.11.0/insight/tests/testthat/test-model_info.R |only insight-0.11.0/insight/tests/testthat/test-multinom.R | 6 insight-0.11.0/insight/tests/testthat/test-mvrstanarm.R | 2 insight-0.11.0/insight/tests/testthat/test-namespace.R | 3 insight-0.11.0/insight/tests/testthat/test-negbin.R | 10 insight-0.11.0/insight/tests/testthat/test-nlmer.R | 8 insight-0.11.0/insight/tests/testthat/test-offset.R |only insight-0.11.0/insight/tests/testthat/test-ols.R | 5 insight-0.11.0/insight/tests/testthat/test-plm.R | 5 insight-0.11.0/insight/tests/testthat/test-polr.R | 5 insight-0.11.0/insight/tests/testthat/test-psm.R | 9 insight-0.11.0/insight/tests/testthat/test-rlmer.R | 8 insight-0.11.0/insight/tests/testthat/test-rms.R | 6 insight-0.11.0/insight/tests/testthat/test-rq.R | 3 insight-0.11.0/insight/tests/testthat/test-rqss.R | 5 insight-0.11.0/insight/tests/testthat/test-rstanarm.R | 12 insight-0.11.0/insight/tests/testthat/test-spatial.R | 3 insight-0.11.0/insight/tests/testthat/test-speedglm.R | 6 insight-0.11.0/insight/tests/testthat/test-speedlm.R | 8 insight-0.11.0/insight/tests/testthat/test-standardize_names.R |only insight-0.11.0/insight/tests/testthat/test-survey.R | 5 insight-0.11.0/insight/tests/testthat/test-survfit.R | 4 insight-0.11.0/insight/tests/testthat/test-survreg.R | 38 insight-0.11.0/insight/tests/testthat/test-tobit.R | 9 insight-0.11.0/insight/tests/testthat/test-truncreg.R | 5 insight-0.11.0/insight/tests/testthat/test-vgam.R | 8 insight-0.11.0/insight/tests/testthat/test-vglm.R | 6 insight-0.11.0/insight/tests/testthat/test-zeroinfl.R | 4 143 files changed, 2702 insertions(+), 1040 deletions(-)
Title: Handling HL7 FHIR Resources in R
Description: Useful tools for conveniently downloading FHIR resources in xml format
and converting them to R data frames. The package uses FHIR-search to download bundles
from a FHIR server, provides functions to save and read xml-files containing such bundles
and allows flattening the bundles to data.frames using XPath expressions.
Author: Thomas Peschel [aut, cre],
Julia Gantner [aut] (<https://orcid.org/0000-0003-1568-5893>),
Jens Przybilla [aut],
Frank Meineke [aut] (<https://orcid.org/0000-0002-9256-7543>)
Maintainer: Thomas Peschel <tpeschel@imise.uni-leipzig.de>
Diff between fhircrackr versions 0.2.0 dated 2020-10-19 and 0.2.1 dated 2020-11-24
DESCRIPTION | 10 - MD5 | 14 +- NEWS.md | 14 ++ R/design.R | 12 +- R/fhircrack.R | 51 +++++---- R/helpers.R | 2 man/fhir_melt.Rd | 2 vignettes/fhircrackr.html | 246 +++++++++++++++++++++++++++------------------- 8 files changed, 209 insertions(+), 142 deletions(-)
Title: Comparative 'Phylogenetic' Analyses of Diversification
Description: Contains a number of comparative 'phylogenetic' methods,
mostly focusing on analysing diversification and character
evolution. Contains implementations of 'BiSSE' (Binary State
'Speciation' and Extinction) and its unresolved tree extensions,
'MuSSE' (Multiple State 'Speciation' and Extinction), 'QuaSSE',
'GeoSSE', and 'BiSSE-ness' Other included methods include Markov
models of discrete and continuous trait evolution and constant rate
'speciation' and extinction.
Author: Richard G. FitzJohn [aut, cre],
Emma Goldberg [aut],
Karen Magnuson-Ford [aut],
Roger Sidje [aut]
Maintainer: Richard G. FitzJohn <rich.fitzjohn@gmail.com>
Diff between diversitree versions 0.9-14 dated 2020-09-04 and 0.9-15 dated 2020-11-24
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- build/partial.rdb |binary configure | 1 + configure.ac | 1 + 5 files changed, 9 insertions(+), 7 deletions(-)
Title: Classical Age-Depth Modelling of Cores from Deposits
Description: Performs 'classical' age-depth modelling of dated sediment deposits - prior to applying more sophisticated techniques such as Bayesian age-depth modelling. Any radiocarbon dated depths are calibrated. Age-depth models are constructed by sampling repeatedly from the dated levels, each time drawing age-depth curves. Model types include linear interpolation, linear or polynomial regression, and a range of splines. See Blaauw (2010). <doi:10.1016/j.quageo.2010.01.002>.
Author: Maarten Blaauw [aut, cre],
J. Andres Christen [ctb],
Judith Esquivel Vazquez [ctb],
Simon Goring [ctb]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between clam versions 2.3.5 dated 2020-08-10 and 2.3.7 dated 2020-11-24
clam-2.3.5/clam/inst/extdata/IntCal20.14C |only clam-2.3.5/clam/inst/extdata/Marine20.14C |only clam-2.3.5/clam/inst/extdata/SHCal20.14C |only clam-2.3.5/clam/inst/extdata/postbomb_NH1.14C |only clam-2.3.5/clam/inst/extdata/postbomb_NH2.14C |only clam-2.3.5/clam/inst/extdata/postbomb_NH3.14C |only clam-2.3.5/clam/inst/extdata/postbomb_SH1-2.14C |only clam-2.3.5/clam/inst/extdata/postbomb_SH3.14C |only clam-2.3.5/clam/man/age.pMC.Rd |only clam-2.3.5/clam/man/copyCalibrationCurve.Rd |only clam-2.3.5/clam/man/pMC.age.Rd |only clam-2.3.7/clam/DESCRIPTION | 10 - clam-2.3.7/clam/MD5 | 35 +---- clam-2.3.7/clam/NAMESPACE | 7 - clam-2.3.7/clam/NEWS.md | 9 + clam-2.3.7/clam/R/calibrate.R | 158 ++++++------------------ clam-2.3.7/clam/R/clam.R | 71 +++++----- clam-2.3.7/clam/R/models.R | 60 ++++----- clam-2.3.7/clam/R/readwrite.R | 50 +++---- clam-2.3.7/clam/man/calBP.14C.Rd | 11 + clam-2.3.7/clam/man/calibrate.Rd | 17 +- clam-2.3.7/clam/man/clam.Rd | 31 +--- clam-2.3.7/clam/man/mix.calibrationcurves.Rd | 9 - clam-2.3.7/clam/man/student.t.Rd | 5 24 files changed, 202 insertions(+), 271 deletions(-)
Title: Subset Partitioning via Anticlustering
Description: The method of anticlustering partitions a pool of
elements into groups (i.e., anticlusters) in such a way that the
between-group similarity is maximized and -- at the same time -- the
within-group heterogeneity is maximized. This reverses the logic of
cluster analysis that strives for high within-group homogeneity and
low similarity of the different groups. Computationally,
anticlustering is accomplished by maximizing instead of minimizing a
clustering objective function, such as the intra-cluster variance
(used in k-means clustering) or the sum of pairwise distances within
clusters. The function anticlustering() implements exact and
heuristic anticlustering algorithms as described in Papenberg and Klau
(2020; <doi:10.1037/met0000301>). The exact approach requires that the
GNU linear programming kit
(<https://www.gnu.org/software/glpk/glpk.html>) is available and the R
package 'Rglpk' (<https://cran.R-project.org/package=Rglpk>) is
installed. Some other functions are available to solve classical
clustering problems. The function balanced_clustering() applies a
cluster analysis under size constraints, i.e., creates equal-sized
clusters. The function matching() can be used for (unrestricted,
bipartite, or K-partite) matching. The function wce() can be used
optimally solve the (weighted) cluster editing problem, also known as
correlation clustering, clique partitioning problem or transitivity
clustering.
Author: Martin Papenberg [aut, cre] (<https://orcid.org/0000-0002-9900-4268>),
Meik Michalke [ctb] (centroid based clustering algorithm),
Gunnar W. Klau [ths],
Juliane V. Tkotz [ctb] (package logo)
Maintainer: Martin Papenberg <martin.papenberg@hhu.de>
Diff between anticlust versions 0.5.3 dated 2020-09-25 and 0.5.6 dated 2020-11-24
DESCRIPTION | 10 +-- MD5 | 42 ++++++++++----- NAMESPACE | 3 + R/anticlust.R |only R/c-anticlustering.R |only R/input-validation.R | 63 ++++++++++++++-------- R/plotting.R | 17 ++++-- R/repeated-exchange.R | 8 +- R/sample-by-category.R | 76 +++++++++++++++++++++++---- R/wrapper-anticlustering.R | 91 +++++++++++++++++---------------- build/vignette.rds |binary inst/doc/stimulus-selection.html | 42 +++++++-------- man/anticlust.Rd |only man/anticlustering.Rd | 32 +++++++---- man/categorical_sampling.Rd | 4 + src |only tests/testthat/test-c-implementation.R |only tests/testthat/test-distance-input.R | 46 +++++++++------- tests/testthat/test-kplus-criterion.R | 17 ++++++ tests/testthat/test-preclustering.R |only tests/testthat/test-standardize.R |only 21 files changed, 295 insertions(+), 156 deletions(-)
Title: Robust Econometric Inference
Description: Drawing statistical inference on the coefficients
of a short- or long-horizon predictive regression with persistent
regressors by using the IVX method of Magdalinos and Phillips (2009)
<doi:10.1017/S0266466608090154> and Kostakis, Magdalinos and
Stamatogiannis (2015) <doi:10.1093/rfs/hhu139>.
Author: Kostas Vasilopoulos [cre, aut],
Efthymios Pavlidis [aut]
Maintainer: Kostas Vasilopoulos <k.vasilopoulo@gmail.com>
Diff between ivx versions 1.0.0 dated 2019-05-04 and 1.1.0 dated 2020-11-24
ivx-1.0.0/ivx/R/utils-pipe.R |only ivx-1.0.0/ivx/man/pipe.Rd |only ivx-1.0.0/ivx/tests/testthat/test-ivx_fit.R |only ivx-1.1.0/ivx/DESCRIPTION | 16 ivx-1.1.0/ivx/MD5 | 64 ++- ivx-1.1.0/ivx/NAMESPACE | 54 ++- ivx-1.1.0/ivx/NEWS.md |only ivx-1.1.0/ivx/R/ac_test.R |only ivx-1.1.0/ivx/R/auto-ar.R |only ivx-1.1.0/ivx/R/data.R | 36 +- ivx-1.1.0/ivx/R/extract-texreg-methods.R |only ivx-1.1.0/ivx/R/ivx-package.R | 9 ivx-1.1.0/ivx/R/ivx.R | 468 ++++++++++++++++++-------- ivx-1.1.0/ivx/R/ivx_ar.R |only ivx-1.1.0/ivx/R/methods.R |only ivx-1.1.0/ivx/R/step-methods.R |only ivx-1.1.0/ivx/R/utils.R |only ivx-1.1.0/ivx/README.md | 85 +++- ivx-1.1.0/ivx/build |only ivx-1.1.0/ivx/data/kms.rda |only ivx-1.1.0/ivx/data/kms_quarterly.rda |only ivx-1.1.0/ivx/data/ylpc.rda |only ivx-1.1.0/ivx/inst/WORDLIST | 24 + ivx-1.1.0/ivx/man/ac_test.Rd |only ivx-1.1.0/ivx/man/ac_test_.Rd |only ivx-1.1.0/ivx/man/delta.Rd | 2 ivx-1.1.0/ivx/man/extract.ivx.Rd |only ivx-1.1.0/ivx/man/figures |only ivx-1.1.0/ivx/man/ivx-package.Rd | 9 ivx-1.1.0/ivx/man/ivx.Rd | 95 +++-- ivx-1.1.0/ivx/man/ivx_ar.Rd |only ivx-1.1.0/ivx/man/ivx_ar_fit.Rd |only ivx-1.1.0/ivx/man/ivx_fit.Rd | 13 ivx-1.1.0/ivx/man/kms.Rd |only ivx-1.1.0/ivx/man/kms_quarterly.Rd |only ivx-1.1.0/ivx/man/monthly.Rd | 25 - ivx-1.1.0/ivx/man/quarterly.Rd | 25 - ivx-1.1.0/ivx/man/summary.ivx.Rd | 8 ivx-1.1.0/ivx/man/summary.ivx_ar.Rd |only ivx-1.1.0/ivx/man/vcov.ivx.Rd | 2 ivx-1.1.0/ivx/man/ylpc.Rd |only ivx-1.1.0/ivx/src/ivx_fit_cpp.cpp | 11 ivx-1.1.0/ivx/tests/testthat/test-ac_test.R |only ivx-1.1.0/ivx/tests/testthat/test-ivx-ar.R |only ivx-1.1.0/ivx/tests/testthat/test-ivx.R |only ivx-1.1.0/ivx/tests/testthat/test-methods.R | 28 + ivx-1.1.0/ivx/tests/testthat/test-warn-stop.R | 16 47 files changed, 687 insertions(+), 303 deletions(-)
Title: 'Compressive' Hierarchical Kernel Clustering Toolbox
Description: Routines for efficient cluster analysis of large scale data. This package implements the 'CHICKN'
clustering algorithm (see 'Permiakova' 'et' 'al.' (2020) "'CHICKN': Extraction of 'peptide' 'chromatographic'
'elution' profiles from large scale mass 'spectrometry' data by means of 'Wasserstein' 'compressive' hierarchical
cluster analysis"). Functions for data compression, hierarchical clustering and post processing are provided.
Author: Olga Permiakova [aut, cre],
Romain Guibert [aut],
Thomas Burger [aut]
Maintainer: Olga Permiakova <olga.permiakova@gmail.com>
Diff between chickn versions 1.2.2 dated 2020-11-12 and 1.2.3 dated 2020-11-24
chickn-1.2.2/chickn/README.md |only chickn-1.2.3/chickn/DESCRIPTION | 21 ++++++++++----------- chickn-1.2.3/chickn/MD5 | 23 +++++++++++------------ chickn-1.2.3/chickn/R/CHICKN_W1.R | 7 +++++-- chickn-1.2.3/chickn/R/DB_funR.R | 12 ++++++++++++ chickn-1.2.3/chickn/R/DrawFreq.R | 12 ++++++++++++ chickn-1.2.3/chickn/R/HCC_parallel.R | 6 ++++++ chickn-1.2.3/chickn/R/Sketch.R | 6 ++++++ chickn-1.2.3/chickn/R/zzz.R | 16 ++++++++++------ chickn-1.2.3/chickn/build/partial.rdb |binary chickn-1.2.3/chickn/inst/REFERENCES.bib | 1 - chickn-1.2.3/chickn/man/CHICKN_W1.Rd | 5 +++-- chickn-1.2.3/chickn/man/chickn.Rd | 14 ++++++++------ 13 files changed, 83 insertions(+), 40 deletions(-)
Title: Parallel Use of Statistical Packages in Teaching
Description: When teaching statistics, it can often be desirable to
uncouple the content from specific software packages. To ease such
efforts, the Rosetta Stats website (<https://rosettastats.com>) allows
comparing analyses in different packages. This package is the companion
to the Rosetta Stats website, aiming to provide functions that produce
output that is similar to output from other statistical packages, thereby
facilitating 'software-agnostic' teaching of statistics.
Author: Gjalt-Jorn Peters [aut, cre] (<https://orcid.org/0000-0002-0336-9589>),
Ron Pat-El [ctb] (<https://orcid.org/0000-0002-4742-0163>),
Peter Verboon [ctb] (<https://orcid.org/0000-0001-8656-0890>),
Melissa Gordon Wolf [ctb] (<https://orcid.org/0000-0001-7677-0659>)
Maintainer: Gjalt-Jorn Peters <gjalt-jorn@userfriendlyscience.com>
Diff between rosetta versions 0.3.0 dated 2020-11-12 and 0.3.1 dated 2020-11-24
DESCRIPTION | 20 ++-- MD5 | 34 ++++--- NAMESPACE | 6 + R/dataReduction.R | 110 ++++++++++++++++++------ R/descr.R |only R/factoranalysisjmv.b.R |only R/factoranalysisjmv.h.R |only R/histogram.R | 31 ++++++ R/logRegr.R | 30 ++++++ R/opts.R | 2 R/regr.R | 17 +-- inst/partials/_rosettaDataReduction_partial.Rmd | 32 ++++++ inst/partials/_rosettaDescr_partial.Rmd |only inst/partials/_rosettaLogRegr_partial.Rmd | 40 ++++++-- inst/partials/_rosettaRegr_partial.Rmd | 28 ++---- man/factorAnalysisjmv.Rd |only man/histogram.Rd |only man/rosettaDataReduction.Rd | 18 ++- man/rosettaDescr.Rd |only man/rosettaLogRegr.Rd | 4 tests |only 21 files changed, 282 insertions(+), 90 deletions(-)
Title: Perform Monothetic Clustering with Extensions to Circular Data
Description: Implementation of the Monothetic Clustering
algorithm (Chavent, 1998 <doi:10.1016/S0167-8655(98)00087-7>) on
continuous data sets. A lot of extensions are included in the package,
including applying Monothetic clustering on data sets with circular
variables, visualizations with the results, and permutation and
cross-validation based tests to support the decision on the number of
clusters.
Author: Tan Tran [aut, cre] (<https://orcid.org/0000-0001-9881-6339>),
Brian McGuire [aut],
Mark Greenwood [aut] (<https://orcid.org/0000-0001-6933-1201>)
Maintainer: Tan Tran <vinhtantran@gmail.com>
Diff between monoClust versions 1.1.0 dated 2020-11-17 and 1.2.0 dated 2020-11-24
monoClust-1.1.0/monoClust/R/mono_utils.R |only monoClust-1.1.0/monoClust/R/plot_utils.R |only monoClust-1.2.0/monoClust/DESCRIPTION | 17 ++- monoClust-1.2.0/monoClust/MD5 | 91 +++++++++++---------- monoClust-1.2.0/monoClust/NAMESPACE | 20 +++- monoClust-1.2.0/monoClust/NEWS.md | 22 ++++- monoClust-1.2.0/monoClust/R/MonoClust.R | 47 ++++------ monoClust-1.2.0/monoClust/R/MonoClust.object.R |only monoClust-1.2.0/monoClust/R/as_MonoClust.R |only monoClust-1.2.0/monoClust/R/circ_arith.R |only monoClust-1.2.0/monoClust/R/circ_dist.R | 5 - monoClust-1.2.0/monoClust/R/cv.test.R | 14 +-- monoClust-1.2.0/monoClust/R/ggcv.R | 9 +- monoClust-1.2.0/monoClust/R/ggpcp.R | 15 +-- monoClust-1.2.0/monoClust/R/inertia_calc.R |only monoClust-1.2.0/monoClust/R/is_MonoClust.R |only monoClust-1.2.0/monoClust/R/medoid.R |only monoClust-1.2.0/monoClust/R/perm.test.R | 12 +- monoClust-1.2.0/monoClust/R/plot.MonoClust.R | 19 ++-- monoClust-1.2.0/monoClust/R/plot.cv.MonoClust.R | 12 +- monoClust-1.2.0/monoClust/R/predict.MonoClust.R | 11 -- monoClust-1.2.0/monoClust/R/print.MonoClust.R | 66 +-------------- monoClust-1.2.0/monoClust/R/utils.R |only monoClust-1.2.0/monoClust/README.md | 5 - monoClust-1.2.0/monoClust/build/partial.rdb |binary monoClust-1.2.0/monoClust/inst/doc/monoclust.R | 1 monoClust-1.2.0/monoClust/inst/doc/monoclust.Rmd | 1 monoClust-1.2.0/monoClust/inst/doc/monoclust.html | 45 +++++----- monoClust-1.2.0/monoClust/man/MonoClust.object.Rd | 6 - monoClust-1.2.0/monoClust/man/as_MonoClust.Rd |only monoClust-1.2.0/monoClust/man/centroid.Rd | 2 monoClust-1.2.0/monoClust/man/circ_arith.Rd | 2 monoClust-1.2.0/monoClust/man/create_labels.Rd | 2 monoClust-1.2.0/monoClust/man/cv.test.Rd | 4 monoClust-1.2.0/monoClust/man/error_bar.Rd | 56 ++++++------ monoClust-1.2.0/monoClust/man/find_closest.Rd | 2 monoClust-1.2.0/monoClust/man/find_split.Rd | 14 --- monoClust-1.2.0/monoClust/man/ggcv.Rd | 3 monoClust-1.2.0/monoClust/man/inertia_calc.Rd | 20 +++- monoClust-1.2.0/monoClust/man/is_MonoClust.Rd |only monoClust-1.2.0/monoClust/man/medoid.Rd | 19 +++- monoClust-1.2.0/monoClust/man/monoClust-package.Rd | 1 monoClust-1.2.0/monoClust/man/new_node.Rd | 2 monoClust-1.2.0/monoClust/man/plot.MonoClust.Rd | 4 monoClust-1.2.0/monoClust/man/plot_prep_branch.Rd | 2 monoClust-1.2.0/monoClust/man/plot_prep_node.Rd | 2 monoClust-1.2.0/monoClust/man/plot_tree.Rd | 2 monoClust-1.2.0/monoClust/man/predict.MonoClust.Rd | 3 monoClust-1.2.0/monoClust/man/text_tree.Rd | 4 monoClust-1.2.0/monoClust/man/tree_depth.Rd | 10 +- monoClust-1.2.0/monoClust/man/tree_walk.Rd | 42 ++++----- monoClust-1.2.0/monoClust/vignettes/monoclust.Rmd | 1 52 files changed, 306 insertions(+), 309 deletions(-)
Title: Brazilian COVID-19 Pandemic Data
Description: Set of functions to import COVID-19 pandemic data into R. The Brazilian COVID-19 data, obtained from the official Brazilian repository at <https://covid.saude.gov.br/>, is available at country, region, state, and city-levels. The package also downloads the world-level COVID-19 data from the John Hopkins University's repository.
Author: Fabio Demarqui [aut, cre],
Cristiano Santos [aut],
Matheus Costa [ctb]
Maintainer: Fabio Demarqui <fndemarqui@est.ufmg.br>
Diff between covid19br versions 0.1.0 dated 2020-09-29 and 0.1.1 dated 2020-11-24
DESCRIPTION | 9 -- MD5 | 11 +- NAMESPACE | 1 NEWS.md |only R/covid19br.R | 1 R/downloadData.R | 233 +++++++++++++++++++++++++++++++------------------------ README.md |only inst |only 8 files changed, 146 insertions(+), 109 deletions(-)
Title: Biodiversity Assessment Tools
Description: Includes algorithms to assess alpha and beta
diversity in all their dimensions (taxon, phylogenetic and functional
diversity), whether communities are completely sampled or not. It allows
performing a number of analyses based on either species identities or
phylogenetic/functional trees or functional kernel n-dimensional hypervolumes
depicting species relationships.
Author: Pedro Cardoso, Stefano Mammola, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>
Diff between BAT versions 2.3.0 dated 2020-10-28 and 2.4.0 dated 2020-11-24
DESCRIPTION | 8 - MD5 | 8 + NAMESPACE | 2 R/BAT.R | 173 ++++++++++++++++++++++++++++++++---- man/evenness.contribution.Rd |only man/kernel.evenness.contribution.Rd |only 6 files changed, 168 insertions(+), 23 deletions(-)
Title: Data and Tools for Analyzing the Pali Canon
Description: Provides access to the complete Pali Canon, or
Tipitaka, the canonical scripture for Theravadin Buddhists
worldwide. Based on the Chattha Sangayana Tipitaka version
4 (Vipassana Research Institute, 1990).
Author: Dan Zigmond [aut, cre]
Maintainer: Dan Zigmond <djz@shmonk.com>
Diff between tipitaka versions 0.1.0 dated 2020-09-22 and 0.1.1 dated 2020-11-24
DESCRIPTION | 17 ++-- MD5 | 44 ++++++----- NAMESPACE | 1 NEWS.md | 4 + R/cpp11.R |only R/pali-sort.R | 136 +++++++++++++++--------------------- R/tipitaka-docs.R | 2 R/tipitaka-package.R |only README.md | 50 ++++++++++++- data/abhidhamma_pitaka.rda |binary data/pali_alphabet.rda |binary data/sati_sutta_long.rda |binary data/sati_sutta_raw.rda |binary data/sutta_pitaka.rda |binary data/tipitaka_long.rda |binary data/tipitaka_names.rda |binary data/tipitaka_raw.rda |binary data/tipitaka_wide.rda |binary data/vinaya_pitaka.rda |binary man/figures/README-kmeans-1.png |binary man/figures/README-wordclouds-1.png |binary man/pali_lt.Rd | 1 man/pali_sort.Rd | 12 +-- src |only 24 files changed, 152 insertions(+), 115 deletions(-)
Title: Stacked Elastic Net
Description: Implements stacked elastic net regression (Rauschenberger 2020, <doi:10.1093/bioinformatics/btaa535>). The elastic net generalises ridge and lasso regularisation (Zou 2005, <doi:10.1111/j.1467-9868.2005.00503.x>). Instead of fixing or tuning the mixing parameter alpha, we combine multiple alpha by stacked generalisation (Wolpert 1992 <doi:10.1016/S0893-6080(05)80023-1>).
Author: Armin Rauschenberger [aut, cre]
Maintainer: Armin Rauschenberger <armin.rauschenberger@uni.lu>
Diff between starnet versions 0.0.5 dated 2020-11-09 and 0.0.6 dated 2020-11-24
DESCRIPTION | 6 ++-- MD5 | 28 +++++++++++------------ R/functions.R | 59 +++++++++++++++++++++++++++++++++++++++++++------ R/pkgname.R | 31 ++++++++++++++++++++++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/script.html | 4 +-- man/coef.starnet.Rd | 11 ++++++++- man/cv.starnet.Rd | 5 ++-- man/predict.starnet.Rd | 11 ++++++++- man/print.starnet.Rd | 11 ++++++++- man/starnet-package.Rd | 29 ------------------------ man/starnet.Rd | 10 +++++++- man/weights.starnet.Rd | 11 ++++++++- tests/testthat/test.R | 2 + 15 files changed, 152 insertions(+), 66 deletions(-)
Title: Species Distribution Model Selection
Description: User-friendly framework that enables the training and the
evaluation of species distribution models (SDMs). The package implements
functions for data driven variable selection and model tuning and includes
numerous utilities to display the results. All the functions used to select
variables or to tune model hyperparameters have an interactive real-time
chart displayed in the 'RStudio' viewer pane during their execution.
Author: Sergio Vignali [aut, cre] (<https://orcid.org/0000-0002-3390-5442>),
Arnaud Barras [aut] (<https://orcid.org/0000-0003-0850-6965>),
Veronika Braunisch [aut] (<https://orcid.org/0000-0001-7035-4662>),
Conservation Biology - University of Bern [fnd]
Maintainer: Sergio Vignali <sergio.vignali@iee.unibe.ch>
Diff between SDMtune versions 1.1.2 dated 2020-10-02 and 1.1.3 dated 2020-11-24
DESCRIPTION | 10 +++++----- MD5 | 28 ++++++++++++++-------------- NEWS.md | 3 +++ R/SDMmodel2MaxEnt.R | 2 +- R/maxentTh.R | 2 +- R/maxentVarImp.R | 2 +- R/reduceVar.R | 2 +- R/train.R | 2 +- R/varSel.R | 2 +- man/SDMmodel2MaxEnt.Rd | 2 +- man/maxentTh.Rd | 2 +- man/maxentVarImp.Rd | 2 +- man/reduceVar.Rd | 2 +- man/train.Rd | 2 +- man/varSel.Rd | 2 +- 15 files changed, 34 insertions(+), 31 deletions(-)
Title: Robust Model-Based Clustering
Description: Performs robust cluster analysis allowing for outliers and noise that cannot be fitted by any cluster. The data are modelled by a mixture of Gaussian distributions and a noise component, which is an improper uniform distribution covering the whole Euclidean space. Parameters are estimated by (pseudo) maximum likelihood. This is fitted by a EM-type algorithm. See Coretto and Hennig (2016) <doi:10.1080/01621459.2015.1100996>, and Coretto and Hennig (2017) <https://jmlr.org/papers/v18/16-382.html>.
Author: Pietro Coretto [aut, cre],
Christian Hennig [aut]
Maintainer: Pietro Coretto <pcoretto@unisa.it>
Diff between otrimle versions 1.3 dated 2019-09-24 and 1.6 dated 2020-11-24
otrimle-1.3/otrimle/ChangeLog |only otrimle-1.6/otrimle/DESCRIPTION | 17 ++--- otrimle-1.6/otrimle/MD5 | 28 ++++---- otrimle-1.6/otrimle/NEWS |only otrimle-1.6/otrimle/R/ecm.R | 26 ++++--- otrimle-1.6/otrimle/R/init.R | 88 +++++++++++++++++++++++++- otrimle-1.6/otrimle/R/otrimle.R | 105 ++++++++++++++++++++------------ otrimle-1.6/otrimle/R/plotting.R | 97 +++++++++++++++++++---------- otrimle-1.6/otrimle/R/printers.R | 8 ++ otrimle-1.6/otrimle/R/rimle.R | 57 +++++++++++------ otrimle-1.6/otrimle/inst/CITATION | 2 otrimle-1.6/otrimle/man/InitClust.Rd | 18 +++-- otrimle-1.6/otrimle/man/otrimle.Rd | 81 ++++++++++++++++++++---- otrimle-1.6/otrimle/man/plot.otrimle.Rd | 5 - otrimle-1.6/otrimle/man/plot.rimle.Rd | 3 otrimle-1.6/otrimle/man/rimle.Rd | 51 ++++++++++----- 16 files changed, 415 insertions(+), 171 deletions(-)
Title: Bayesian Calculation of Region-Specific Fixation Index to Detect
Local Adaptation
Description: An R implementation of an extension of the 'BayeScan' software (Foll, 2008) <DOI:10.1534/genetics.108.092221> for codominant markers, adding the option to group individual SNPs into pre-defined blocks. A typical application of this new approach is the identification of genomic regions, genes, or gene sets containing one or more SNPs that evolved under directional selection.
Author: Bastian Pfeifer
Maintainer: Bastian Pfeifer <bastianxpfeifer@gmail.com>
Diff between BlockFeST versions 1.6 dated 2018-05-06 and 1.8 dated 2020-11-24
DESCRIPTION | 10 ++++------ MD5 | 15 +++++++++------ NEWS |only R/slim.R | 11 +++++++---- R/update_slim.R | 29 +++++++++++++++++++++++++++-- README.md |only build/vignette.rds |binary inst/CITATION |only inst/doc/Input_format.pdf |binary src/update_group_C.c | 16 ++++++++++------ 10 files changed, 57 insertions(+), 24 deletions(-)
Title: Sparse Multi-Type Regularized Feature Modeling
Description: Implementation of the SMuRF algorithm of Devriendt et al. (2018) <arXiv:1810.03136> to fit generalized linear models (GLMs) with multiple types of predictors via regularized maximum likelihood.
Author: Tom Reynkens [aut, cre] (<https://orcid.org/0000-0002-5516-5107>),
Sander Devriendt [aut],
Katrien Antonio [aut]
Maintainer: Tom Reynkens <tomreynkens@hotmail.com>
Diff between smurf versions 1.0.6 dated 2020-05-16 and 1.0.7 dated 2020-11-24
DESCRIPTION | 12 - MD5 | 16 - R/Penalty_weights.R | 13 + R/plot_lambda.R | 2 build/vignette.rds |binary inst/NEWS.Rd | 16 + inst/doc/smurf.html | 54 ++++- man/glmsmurf.Rd | 540 +++++++++++++++++++++++++-------------------------- man/smurf-package.Rd | 56 ++--- 9 files changed, 390 insertions(+), 319 deletions(-)
Title: A Data Cube 'dplyr' Backend
Description: An implementation of a data cube extracted out of
'dplyr' for backward compatibility.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between cubelyr versions 1.0.0 dated 2020-02-29 and 1.0.1 dated 2020-11-24
DESCRIPTION | 10 +++++----- MD5 | 11 ++++++----- NAMESPACE | 2 ++ NEWS.md |only R/cube.R | 7 +++++++ README.md | 1 + man/nasa.Rd | 4 +++- 7 files changed, 24 insertions(+), 11 deletions(-)
Title: Parametric Survival Simulation with Parameter Uncertainty
Description: Perform survival simulation with parametric survival model generated from 'survreg' function in 'survival' package.
In each simulation coefficients are resampled from variance-covariance matrix of parameter estimates to
capture uncertainty in model parameters.
Prediction intervals of Kaplan-Meier estimates and hazard ratio of treatment effect can be further calculated using simulated survival data.
Author: Kenta Yoshida [aut, cre] (<https://orcid.org/0000-0003-4967-3831>),
Laurent Claret [aut]
Maintainer: Kenta Yoshida <6.kurabupasu@gmail.com>
Diff between survParamSim versions 0.1.2 dated 2020-06-18 and 0.1.3 dated 2020-11-24
DESCRIPTION | 8 - MD5 | 24 +-- NEWS.md | 10 + README.md | 2 build/vignette.rds |binary inst/doc/survParamSim.html | 74 +++++++++- tests/figs/deps.txt | 2 tests/figs/test-calc-km-pi/km-plot-with-sex-and-ph-ecog-as-group.svg | 14 - tests/figs/test-calc-km-pi/km-plot-with-sex-as-trt.svg | 4 tests/figs/test-calc-km-pi/long-sim-time-not-truncating-with-censor.svg | 4 tests/figs/test-calc-km-pi/long-sim-time-truncating-with-censor.svg | 4 tests/figs/test-calc-km-pi/no-observed-km-curves.svg | 4 tests/testthat.R | 2 13 files changed, 112 insertions(+), 40 deletions(-)
Title: Prioritization of Candidate Cancer Subtype Specific Drugs
Description: A systematic biology tool was developed to prioritize cancer subtype-specific drugs by integrating genetic perturbation, drug action, biological pathway, and cancer subtype.
The capabilities of this tool include inferring patient-specific subpathway activity profiles in the context of gene expression profiles with subtype labels, calculating differentially
expressed subpathways based on cultured human cells treated with drugs in the 'cMap' (connectivity map) database, prioritizing cancer subtype specific drugs according to drug-disease
reverse association score based on subpathway, and visualization of results (Castelo (2013) <doi:10.1186/1471-2105-14-7>; Han et al (2019) <doi:10.1093/bioinformatics/btz894>; Lamb and Justin (2006) <DOI:10.1126/science.1132939>).
Author: Xudong Han,
Junwei Han,
Chonghui Liu
Maintainer: Junwei Han <hanjunwei1981@163.com>
Diff between SubtypeDrug versions 0.1.2 dated 2020-09-24 and 0.1.3 dated 2020-11-24
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/plotDScoreHeatmap.R | 30 ++++++++++++++++++++++++------ R/plotDSpwHeatmap.R | 33 +++++++++++++++++++++++++++------ inst/doc/vignette.html | 8 ++++---- man/plotDScoreHeatmap.Rd | 18 ++++++++++++++++++ man/plotDSpwHeatmap.Rd | 15 +++++++++++++++ 7 files changed, 97 insertions(+), 25 deletions(-)
Title: Interface for the 'Finnish Biodiversity Information Facility'
API
Description: A programmatic interface to the 'Finnish Biodiversity Information
Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates
Finnish biodiversity data from multiple sources in a single open access
portal for researchers, citizen scientists, industry and government.
'FinBIF' allows users of biodiversity information to find, access, combine
and visualise data on Finnish plants, animals and microorganisms. The
'finbif' package makes the publicly available data in 'FinBIF' easily
accessible to programmers. Biodiversity information is available on taxonomy
and taxon occurrence. Occurrence data can be filtered by taxon, time,
location and other variables. The data accessed are conveniently
preformatted for subsequent analyses.
Author: LUOMUS - Finnish Museum of Natural History [cph],
William Morris [aut, cre] (<https://orcid.org/0000-0002-8686-4154>)
Maintainer: William Morris <willi@mmorris.email>
Diff between finbif versions 0.3.0 dated 2020-04-23 and 0.3.1 dated 2020-11-24
finbif-0.3.0/finbif/inst/vign/cache/collection-filter_08c382f823459dc0749d8c809ac240d6.RData |only finbif-0.3.0/finbif/inst/vign/cache/collection-filter_08c382f823459dc0749d8c809ac240d6.rdb |only finbif-0.3.0/finbif/inst/vign/cache/collection-filter_08c382f823459dc0749d8c809ac240d6.rdx |only finbif-0.3.0/finbif/inst/vign/cache/quality-filter_49903c08f7e3457a73938ea46b940f13.RData |only finbif-0.3.0/finbif/inst/vign/cache/quality-filter_49903c08f7e3457a73938ea46b940f13.rdb |only finbif-0.3.0/finbif/inst/vign/cache/quality-filter_49903c08f7e3457a73938ea46b940f13.rdx |only finbif-0.3.1/finbif/DESCRIPTION | 14 finbif-0.3.1/finbif/MD5 | 58 finbif-0.3.1/finbif/NEWS.md | 18 finbif-0.3.1/finbif/R/filters.R | 6 finbif-0.3.1/finbif/R/sysdata.rda |binary finbif-0.3.1/finbif/R/variables.R | 6 finbif-0.3.1/finbif/README.md | 22 finbif-0.3.1/finbif/build/vignette.rds |binary finbif-0.3.1/finbif/data/finland_map.rda |binary finbif-0.3.1/finbif/inst/NEWS.Rd | 19 finbif-0.3.1/finbif/inst/doc/finbif.html | 568 +++++---- finbif-0.3.1/finbif/inst/doc/v02_occurrence_data.html | 462 ++++--- finbif-0.3.1/finbif/inst/doc/v03_selecting_variables.html | 316 +++-- finbif-0.3.1/finbif/inst/doc/v04_metadata.html | 550 ++++---- finbif-0.3.1/finbif/inst/doc/v05_filtering.Rmd | 23 finbif-0.3.1/finbif/inst/doc/v05_filtering.html | 625 +++++----- finbif-0.3.1/finbif/inst/doc/v06_plotting.html | 184 ++ finbif-0.3.1/finbif/inst/vign/cache/collection-filter_0c81b8863d977c2d927e5c45540f295e.RData |only finbif-0.3.1/finbif/inst/vign/cache/collection-filter_0c81b8863d977c2d927e5c45540f295e.rdb |only finbif-0.3.1/finbif/inst/vign/cache/collection-filter_0c81b8863d977c2d927e5c45540f295e.rdx |only finbif-0.3.1/finbif/inst/vign/cache/quality-filter_fc0970f9a56837631b5bf6855b358d98.RData |only finbif-0.3.1/finbif/inst/vign/cache/quality-filter_fc0970f9a56837631b5bf6855b358d98.rdb |only finbif-0.3.1/finbif/inst/vign/cache/quality-filter_fc0970f9a56837631b5bf6855b358d98.rdx |only finbif-0.3.1/finbif/inst/vign/v05_filtering.Rmd | 14 finbif-0.3.1/finbif/inst/vign/v05_filtering.md | 23 finbif-0.3.1/finbif/man/filters.Rd | 6 finbif-0.3.1/finbif/man/finbif-package.Rd | 2 finbif-0.3.1/finbif/man/variables.Rd | 6 finbif-0.3.1/finbif/tests/testthat/test-finbif_occurrence.R | 14 finbif-0.3.1/finbif/vignettes/v05_filtering.Rmd | 23 36 files changed, 1705 insertions(+), 1254 deletions(-)
Title: Spatial Forecast Verification
Description: Spatial forecast verification refers to verifying weather forecasts when the verification set (forecast and observations) is on a spatial field, usually a high-resolution gridded spatial field. Most of the functions here require the forecast and observed fields to be gridded and on the same grid. For a thorough review of most of the methods in this package, please see Gilleland et al. (2009) <doi: 10.1175/2009WAF2222269.1>.
Author: Eric Gilleland <EricG@ucar.edu>
Maintainer: Eric Gilleland <EricG@ucar.edu>
Diff between SpatialVx versions 0.7 dated 2020-09-01 and 0.7-1 dated 2020-11-24
COPYING |only DESCRIPTION | 12 ++++++------ MD5 | 5 +++-- R/Gbeta.R | 18 +++++++++++++----- 4 files changed, 22 insertions(+), 13 deletions(-)
Title: Emax Model Analysis with 'Stan'
Description: Perform sigmoidal Emax model fit using 'Stan' in a formula notation, without writing 'Stan' model code.
Author: Kenta Yoshida [aut, cre] (<https://orcid.org/0000-0003-4967-3831>),
Trustees of Columbia University [cph] (src/init.cpp, tools/make_cc.R,
R/stanmodels.R)
Maintainer: Kenta Yoshida <6.kurabupasu@gmail.com>
Diff between rstanemax versions 0.1.2 dated 2020-06-18 and 0.1.3 dated 2020-11-24
rstanemax-0.1.2/rstanemax/tests/testthat/Rplots.pdf |only rstanemax-0.1.3/rstanemax/DESCRIPTION | 8 rstanemax-0.1.3/rstanemax/MD5 | 19 rstanemax-0.1.3/rstanemax/NEWS.md | 12 rstanemax-0.1.3/rstanemax/R/stanemax-methods.R | 6 rstanemax-0.1.3/rstanemax/build/vignette.rds |binary rstanemax-0.1.3/rstanemax/inst/doc/emaxmodel.R | 3 rstanemax-0.1.3/rstanemax/inst/doc/emaxmodel.Rmd | 8 rstanemax-0.1.3/rstanemax/inst/doc/emaxmodel.html | 401 +++++++++++--------- rstanemax-0.1.3/rstanemax/tests/testthat.R | 2 rstanemax-0.1.3/rstanemax/vignettes/emaxmodel.Rmd | 8 11 files changed, 274 insertions(+), 193 deletions(-)
Title: Systematic Conservation Prioritization in R
Description: Conservation prioritization using integer
programming techniques. To solve large-scale problems, users
should install the 'gurobi' optimizer
(available from <https://www.gurobi.com/>).
Author: Jeffrey O Hanson [aut] (<https://orcid.org/0000-0002-4716-6134>),
Richard Schuster [aut, cre] (<https://orcid.org/0000-0003-3191-7869>),
Nina Morrell [aut],
Matthew Strimas-Mackey [aut] (<https://orcid.org/0000-0001-8929-7776>),
Matthew E Watts [aut],
Peter Arcese [aut] (<https://orcid.org/0000-0002-8097-482X>),
Joseph Bennett [aut] (<https://orcid.org/0000-0002-3901-9513>),
Hugh P Possingham [aut] (<https://orcid.org/0000-0001-7755-996X>)
Maintainer: Richard Schuster <richard.schuster@glel.carleton.ca>
Diff between prioritizr versions 5.0.2 dated 2020-07-30 and 5.0.3 dated 2020-11-24
DESCRIPTION | 32 MD5 | 645 NAMESPACE | 409 R/ArrayParameter-proto.R | 288 R/Collection-proto.R | 334 R/ConservationModifier-proto.R | 362 R/ConservationProblem-proto.R | 1230 R/Constraint-proto.R | 48 R/Decision-proto.R | 50 R/Id.R | 114 R/MiscParameter-proto.R | 208 R/Objective-proto.R | 44 R/OptimizationProblem-methods.R | 622 R/OptimizationProblem-proto.R | 402 R/Parameter-proto.R | 152 R/Parameters-proto.R | 330 R/Penalty-proto.R | 50 R/Portfolio-proto.R | 188 R/RcppExports.R | 382 R/ScalarParameter-proto.R | 258 R/Solver-proto.R | 296 R/Target-proto.R | 48 R/add_absolute_targets.R | 432 R/add_binary_decisions.R | 160 R/add_boundary_penalties.R | 658 R/add_connectivity_penalties.R | 1080 R/add_contiguity_constraints.R | 616 R/add_cplex_solver.R |only R/add_cuts_portfolio.R | 252 R/add_default_decisions.R | 34 R/add_default_objective.R | 18 R/add_default_portfolio.R | 32 R/add_default_solver.R | 103 R/add_default_targets.R | 18 R/add_extra_portfolio.R | 208 R/add_feature_contiguity_constraints.R | 748 R/add_feature_weights.R | 564 R/add_gap_portfolio.R | 268 R/add_gurobi_solver.R | 407 R/add_linear_penalties.R | 712 R/add_locked_in_constraints.R | 732 R/add_locked_out_constraints.R | 610 R/add_loglinear_targets.R | 313 R/add_lpsymphony_solver.R | 309 R/add_mandatory_allocation_constraints.R | 198 R/add_manual_bounded_constraints.R | 472 R/add_manual_locked_constraints.R | 492 R/add_manual_targets.R | 636 R/add_max_cover_objective.R | 362 R/add_max_features_objective.R | 314 R/add_max_phylo_div_objective.R | 558 R/add_max_phylo_end_objective.R | 586 R/add_max_utility_objective.R | 292 R/add_min_set_objective.R | 216 R/add_min_shortfall_objective.R | 290 R/add_neighbor_contraints.R | 694 R/add_proportion_decisions.R | 144 R/add_relative_targets.R | 332 R/add_rsymphony_solver.R | 328 R/add_semicontinuous_decisions.R | 168 R/add_shuffle_portfolio.R | 306 R/add_top_portfolio.R | 222 R/adjacency_matrix.R | 346 R/binary_stack.R | 102 R/boundary_matrix.R | 414 R/branch_matrix.R | 114 R/category_layer.R | 104 R/category_vector.R | 156 R/compile.R | 274 R/connectivity_matrix.R | 594 R/constraints.R | 188 R/data.R | 364 R/decisions.R | 160 R/deprecated.R | 154 R/distribute_load.R | 164 R/fast_extract.R | 318 R/feature_abundances.R | 324 R/feature_names.R | 134 R/feature_representation.R | 806 R/ferrier_score.R | 641 R/internal.R | 543 R/intersecting_units.R | 448 R/irreplaceability.R | 226 R/loglinear_interpolation.R | 154 R/magrittr-operators.R | 160 R/marxan_boundary_data_to_matrix.R | 314 R/marxan_problem.R | 728 R/misc.R | 84 R/new_optimization_problem.R | 42 R/number_of_features.R | 152 R/number_of_planning_units.R | 116 R/number_of_total_units.R | 128 R/number_of_zones.R | 154 R/objectives.R | 192 R/package.R | 170 R/parameters.R | 996 R/penalties.R | 176 R/portfolios.R | 216 R/pproto.R | 150 R/predefined_optimization_problem.R | 198 R/presolve_check.R | 578 R/print.R | 216 R/problem.R | 2010 R/proximity_matrix.R | 346 R/rarity_weighted_richness.R | 866 R/replacement_cost.R | 1164 R/rij_matrix.R | 274 R/run_calculations.R | 164 R/sf.R | 12 R/show.R | 140 R/simulate.R | 262 R/solve.R | 770 R/solvers.R | 228 R/targets.R | 150 R/tbl_df.R | 148 R/waiver.R | 62 R/zone_names.R | 140 R/zones.R | 362 R/zzz.R | 62 README.md | 1020 build/vignette.rds |binary inst/doc/gurobi_installation.Rmd | 382 inst/doc/gurobi_installation.html | 1063 inst/doc/prioritizr.Rmd | 1667 inst/doc/prioritizr.html | 3413 - inst/doc/publication_record.Rmd | 104 inst/doc/publication_record.html | 632 inst/doc/saltspring.Rmd | 475 inst/doc/saltspring.html | 1132 inst/doc/tasmania.Rmd | 451 inst/doc/tasmania.html |28490 ------------- inst/doc/zones.Rmd | 646 inst/doc/zones.html | 2171 inst/extdata/input.dat | 110 inst/extdata/simulate_data.R | 356 man/ArrayParameter-class.Rd | 200 man/Collection-class.Rd | 194 man/ConservationModifier-class.Rd | 256 man/ConservationProblem-class.Rd | 594 man/Constraint-class.Rd | 32 man/Decision-class.Rd | 34 man/MiscParameter-class.Rd | 166 man/Objective-class.Rd | 26 man/OptimizationProblem-class.Rd | 248 man/OptimizationProblem-methods.Rd | 288 man/Parameter-class.Rd | 118 man/Parameters-class.Rd | 180 man/Penalty-class.Rd | 34 man/Portfolio-class.Rd | 132 man/ScalarParameter-class.Rd | 182 man/Solver-class.Rd | 198 man/Target-class.Rd | 32 man/add_absolute_targets.Rd | 312 man/add_binary_decisions.Rd | 140 man/add_boundary_penalties.Rd | 496 man/add_connectivity_penalties.Rd | 834 man/add_contiguity_constraints.Rd | 420 man/add_cplex_solver.Rd |only man/add_cuts_portfolio.Rd | 180 man/add_default_decisions.Rd | 38 man/add_default_solver.Rd | 56 man/add_extra_portfolio.Rd | 150 man/add_feature_contiguity_constraints.Rd | 460 man/add_feature_weights.Rd | 426 man/add_gap_portfolio.Rd | 182 man/add_gurobi_solver.Rd | 206 man/add_linear_penalties.Rd | 422 man/add_locked_in_constraints.Rd | 476 man/add_locked_out_constraints.Rd | 472 man/add_loglinear_targets.Rd | 245 man/add_lsymphony_solver.Rd | 176 man/add_mandatory_allocation_constraints.Rd | 148 man/add_manual_bounded_constraints.Rd | 282 man/add_manual_locked_constraints.Rd | 280 man/add_manual_targets.Rd | 410 man/add_max_cover_objective.Rd | 314 man/add_max_features_objective.Rd | 254 man/add_max_phylo_div_objective.Rd | 460 man/add_max_phylo_end_objective.Rd | 464 man/add_max_utility_objective.Rd | 242 man/add_min_set_objective.Rd | 194 man/add_min_shortfall_objective.Rd | 244 man/add_neighbor_constraints.Rd | 384 man/add_proportion_decisions.Rd | 144 man/add_relative_targets.Rd | 306 man/add_rsymphony_solver.Rd | 164 man/add_semicontinuous_decisions.Rd | 160 man/add_shuffle_portfolio.Rd | 176 man/add_top_portfolio.Rd | 154 man/adjacency_matrix.Rd | 230 man/array_parameters.Rd | 270 man/as.Rd | 58 man/as.list.Rd | 38 man/binary_stack.Rd | 84 man/boundary_matrix.Rd | 228 man/branch_matrix.Rd | 92 man/category_layer.Rd | 90 man/category_vector.Rd | 108 man/compile.Rd | 116 man/connectivity_matrix.Rd | 428 man/constraints.Rd | 192 man/decisions.Rd | 164 man/distribute_load.Rd | 138 man/fast_extract.Rd | 138 man/feature_abundances.Rd | 290 man/feature_names.Rd | 80 man/feature_representation.Rd | 478 man/ferrier_score.Rd | 243 man/intersecting_units.Rd | 190 man/irreplaceability.Rd | 228 man/is.Rd | 42 man/loglinear_interpolation.Rd | 144 man/marxan_boundary_data_to_matrix.Rd | 114 man/marxan_problem.Rd | 388 man/matrix_parameters.Rd | 138 man/misc_parameter.Rd | 122 man/new_id.Rd | 70 man/new_optimization_problem.Rd | 48 man/new_waiver.Rd | 64 man/number_of_features.Rd | 86 man/number_of_planning_units.Rd | 74 man/number_of_total_units.Rd | 98 man/number_of_zones.Rd | 90 man/objectives.Rd | 194 man/parameters.Rd | 66 man/penalties.Rd | 180 man/pipe.Rd | 68 man/portfolios.Rd | 216 man/pproto.Rd | 88 man/predefined_optimization_problem.Rd | 142 man/presolve_check.Rd | 368 man/print.Rd | 108 man/prioritizr-deprecated.Rd | 144 man/prioritizr.Rd | 156 man/problem.Rd | 900 man/proximity_matrix.Rd | 224 man/rarity_weighted_richness.Rd | 304 man/replacement_cost.Rd | 446 man/rij_matrix.Rd | 144 man/run_calculations.Rd | 154 man/scalar_parameters.Rd | 244 man/show.Rd | 72 man/sim_data.Rd | 386 man/simulate_cost.Rd | 108 man/simulate_data.Rd | 94 man/simulate_species.Rd | 106 man/solve.Rd | 484 man/solvers.Rd | 230 man/targets.Rd | 140 man/tee.Rd | 80 man/tibble-methods.Rd | 104 man/zone_names.Rd | 84 man/zones.Rd | 204 tests/testthat.R | 36 tests/testthat/test_Id.R | 26 tests/testthat/test_OptimizationProblem.R | 246 tests/testthat/test_Waiver.R | 22 tests/testthat/test_add_absolute_targets.R | 452 tests/testthat/test_add_boundary_penalties.R | 842 tests/testthat/test_add_connectivity_penalties.R | 648 tests/testthat/test_add_contiguity_constraints.R | 542 tests/testthat/test_add_cuts_portfolio.R | 408 tests/testthat/test_add_extra_portfolio.R | 432 tests/testthat/test_add_feature_contiguity_constraints.R | 937 tests/testthat/test_add_feature_weights.R | 767 tests/testthat/test_add_gap_portfolio.R | 432 tests/testthat/test_add_linear_penalties.R | 866 tests/testthat/test_add_locked_in_constraints.R | 1239 tests/testthat/test_add_locked_out_constraints.R | 1230 tests/testthat/test_add_loglinear_targets.R | 196 tests/testthat/test_add_mandatory_allocation_constraints.R | 368 tests/testthat/test_add_manual_bounded_constraints.R | 394 tests/testthat/test_add_manual_locked_constraints.R | 406 tests/testthat/test_add_manual_targets.R | 360 tests/testthat/test_add_max_cover_objective.R | 1042 tests/testthat/test_add_max_features_objective.R | 1204 tests/testthat/test_add_max_phylo_div_objective.R | 1524 tests/testthat/test_add_max_phylo_end_objective.R | 1640 tests/testthat/test_add_max_utility_objective.R | 1062 tests/testthat/test_add_min_set_objective.R | 621 tests/testthat/test_add_min_shortfalls_objective.R | 1190 tests/testthat/test_add_neighbor_constraints.R | 536 tests/testthat/test_add_relative_targets.R | 408 tests/testthat/test_add_shuffle_portfolio.R | 528 tests/testthat/test_add_top_portfolio.R | 432 tests/testthat/test_adjacency_matrix.R | 214 tests/testthat/test_binary_stack.R | 66 tests/testthat/test_boundary_matrix.R | 586 tests/testthat/test_branch_matrix.R | 68 tests/testthat/test_category_layer.R | 78 tests/testthat/test_category_vector.R | 110 tests/testthat/test_compile.R | 206 tests/testthat/test_connectivity_matrix.R | 306 tests/testthat/test_cplex.R |only tests/testthat/test_decisions.R | 440 tests/testthat/test_disribute_load.R | 33 tests/testthat/test_fast_extract.R | 268 tests/testthat/test_feature_abundances.R | 370 tests/testthat/test_feature_representation.R | 880 tests/testthat/test_ferrier_score.R | 374 tests/testthat/test_internal.R | 190 tests/testthat/test_intersecting_units.R | 244 tests/testthat/test_marxan_problem.R | 493 tests/testthat/test_parameters.R | 864 tests/testthat/test_pproto.R | 200 tests/testthat/test_presolve_check.R | 262 tests/testthat/test_problem.R | 2314 - tests/testthat/test_problem_negative.R | 1380 tests/testthat/test_proximity_matrix.R | 406 tests/testthat/test_rarity_weighted_richness.R | 528 tests/testthat/test_replacement_cost.R | 994 tests/testthat/test_rij_matrix.R | 408 tests/testthat/test_simulate.R | 86 tests/testthat/test_solve.R | 816 tests/testthat/test_solvers.R | 980 tests/testthat/test_sp_to_polyset.R | 48 tests/testthat/test_zones.R | 78 vignettes/gurobi_installation.Rmd | 382 vignettes/prioritizr.Rmd | 1667 vignettes/publication_record.Rmd | 104 vignettes/reference-style.csl | 402 vignettes/references.bib | 718 vignettes/saltspring.Rmd | 475 vignettes/tasmania.Rmd | 451 vignettes/zones.Rmd | 646 325 files changed, 60126 insertions(+), 87175 deletions(-)
Title: Create and Evaluate NONMEM Models in a Project Context
Description: Systematically creates and modifies NONMEM(R) control streams. Harvests
NONMEM output, builds run logs, creates derivative data, generates diagnostics.
NONMEM (ICON Development Solutions <http://www.iconplc.com/>) is software for
nonlinear mixed effects modeling. See 'package?nonmemica'.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between nonmemica versions 0.9.6 dated 2020-10-21 and 0.9.7 dated 2020-11-24
DESCRIPTION | 6 +- MD5 | 16 ++--- R/model.R | 7 +- R/runrecord.R | 6 +- R/safejoin.R | 2 build/vignette.rds |binary inst/doc/parameter-table.html | 125 +++++++++++++++++++++++++++++------------- man/as.model.Rd | 2 man/safe_join.data.frame.Rd | 2 9 files changed, 110 insertions(+), 56 deletions(-)
Title: Extreme Value Analysis
Description: General functions for performing extreme value analysis. In particular, allows for inclusion of covariates into the parameters of the extreme-value distributions, as well as estimation through MLE, L-moments, generalized (penalized) MLE (GMLE), as well as Bayes. Inference methods include parametric normal approximation, profile-likelihood, Bayes, and bootstrapping. Some bivariate functionality and dependence checking (e.g., auto-tail dependence function plot, extremal index estimation) is also included. For a tutorial, see Gilleland and Katz (2016) <doi: 10.18637/jss.v072.i08> and for bootstrapping, please see Gilleland (2020) <doi: 10.1175/JTECH-D-20-0070.1>.
Author: Eric Gilleland
Maintainer: Eric Gilleland <ericg@ucar.edu>
Diff between extRemes versions 2.0-12 dated 2020-05-03 and 2.1 dated 2020-11-24
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ man/CarcasonneHeat.Rd | 2 +- man/hwmi.Rd | 2 +- man/hwmid.Rd | 2 +- man/xbooter.Rd | 5 +++++ man/xtibber.Rd | 6 ++++++ 7 files changed, 26 insertions(+), 15 deletions(-)
Title: Helpers for Model Coefficients Tibbles
Description: Provides suite of functions to work with regression
model 'broom::tidy()' tibbles. The suite includes functions to group
regression model terms by variable, insert reference and header rows
for categorical variables, add variable labels, and more.
Author: Joseph Larmarange [aut, cre] (<https://orcid.org/0000-0001-7097-700X>),
Daniel D. Sjoberg [aut] (<https://orcid.org/0000-0003-0862-2018>)
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between broom.helpers versions 1.0.0 dated 2020-09-18 and 1.1.0 dated 2020-11-24
DESCRIPTION | 24 MD5 | 129 +- NAMESPACE | 61 + NEWS.md | 61 + R/broom.helpers-package.R | 38 R/helpers.R |only R/model_get_coefficients_type.R |only R/model_get_model.R |only R/model_get_nlevels.R |only R/model_identify_variables.R | 95 + R/model_list_contrasts.R | 16 R/model_list_terms_levels.R | 149 +- R/model_list_variables.R | 90 + R/reexport.R |only R/select_helpers.R |only R/select_utilities.R |only R/tidy_add_coefficients_type.R |only R/tidy_add_contrasts.R | 12 R/tidy_add_estimate_to_reference_rows.R | 97 + R/tidy_add_header_rows.R | 38 R/tidy_add_reference_rows.R | 44 R/tidy_add_term_labels.R | 33 R/tidy_add_variable_labels.R | 51 R/tidy_and_attach.R | 68 + R/tidy_identify_variables.R | 49 R/tidy_plus_plus.R | 58 - R/tidy_remove_intercept.R | 5 R/tidy_select_variables.R |only README.md | 230 ++-- build/vignette.rds |binary inst/WORDLIST |only inst/doc/tidy.R | 49 inst/doc/tidy.Rmd | 59 - inst/doc/tidy.html | 1085 +++++++++++++++++-- man/dot-clean_backticks.Rd |only man/dot-escape_regex.Rd |only man/dot-formula_list_to_named_list.Rd |only man/dot-generic_selector.Rd |only man/dot-select_to_varnames.Rd |only man/model_get_coefficients_type.Rd |only man/model_get_contrasts.Rd | 3 man/model_get_model.Rd |only man/model_get_model_frame.Rd | 3 man/model_get_model_matrix.Rd | 3 man/model_get_nlevels.Rd |only man/model_get_xlevels.Rd | 3 man/model_identify_variables.Rd | 16 man/model_list_contrasts.Rd | 7 man/model_list_terms_levels.Rd | 40 man/model_list_variables.Rd | 17 man/reexports.Rd | 43 man/select_helpers.Rd |only man/tidy_add_coefficients_type.Rd |only man/tidy_add_contrasts.Rd | 98 - man/tidy_add_estimate_to_reference_rows.Rd | 10 man/tidy_add_header_rows.Rd | 17 man/tidy_add_reference_rows.Rd | 26 man/tidy_add_term_labels.Rd | 25 man/tidy_add_variable_labels.Rd | 12 man/tidy_attach_model.Rd | 14 man/tidy_identify_variables.Rd | 26 man/tidy_plus_plus.Rd | 42 man/tidy_remove_intercept.Rd | 4 man/tidy_select_variables.Rd |only tests/spelling.R |only tests/testthat/test-add_coefficients_type.R |only tests/testthat/test-add_contrasts.R | 41 tests/testthat/test-add_estimate_to_reference_rows.R | 56 tests/testthat/test-add_header_rows.R | 75 - tests/testthat/test-add_reference_rows.R | 42 tests/testthat/test-add_term_labels.R | 19 tests/testthat/test-add_variable_labels.R | 11 tests/testthat/test-attach_and_detach.R | 22 tests/testthat/test-identify_variables.R | 173 ++- tests/testthat/test-select_helpers.R |only tests/testthat/test-select_variables.R |only tests/testthat/test-tidy_plus_plus.R | 290 +++++ vignettes/tidy.Rmd | 59 - 78 files changed, 3088 insertions(+), 650 deletions(-)
Title: Boosted Multivariate Trees for Longitudinal Data
Description: Implements Friedman's gradient descent boosting algorithm for modeling longitudinal response using multivariate tree base learners. Longitudinal response could be continuous, binary, nominal or ordinal. A time-covariate interaction effect is modeled using penalized B-splines (P-splines) with estimated adaptive smoothing parameter. Although the package is design for longitudinal data, it can handle cross-sectional data as well. Implementation details are provided in Pande et al. (2017), Mach Learn <DOI:10.1007/s10994-016-5597-1>.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Amol Pande <amoljpande@gmail.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between boostmtree versions 1.4.1 dated 2019-11-21 and 1.5.0 dated 2020-11-24
DESCRIPTION | 12 MD5 | 52 +-- NAMESPACE | 2 R/boostmtree.R | 576 ++++++++++++++++++++++++++++++++--------- R/boostmtree.news.R | 2 R/generic.predict.boostmtree.R | 424 ++++++++++++++++++++++++++---- R/marginalPlot.R | 81 ++++- R/partialPlot.R | 94 +++++- R/plot.boostmtree.R | 167 ++++++++--- R/predict.boostmtree.R | 4 R/print.boostmtree.R | 68 ++++ R/simLong.R | 2 R/utilities.R | 86 +++++- R/vimp.boostmtree.R | 408 +++++++++++++++++++++-------- R/vimpPlot.R | 53 ++- R/zzz.R | 2 data/AF.RData |binary data/spirometry.RData |binary inst/NEWS | 14 man/AF.Rd | 2 man/boostmtree.Rd | 40 ++ man/boostmtree_package.Rd | 3 man/marginalPlot.Rd | 35 +- man/partialPlot.Rd | 33 +- man/plot.boostmtree.Rd | 4 man/predict.boostmtree.Rd | 17 - man/vimpPlot.Rd | 10 27 files changed, 1705 insertions(+), 486 deletions(-)
Title: Long Term Water Quality Trend Analysis
Description: Enable users to evaluate long-term trends using a Generalized
Additive Modeling (GAM) approach. The model development includes selecting a
GAM structure to describe nonlinear seasonally-varying changes over time,
incorporation of hydrologic variability via either a river flow or salinity,
the use of an intervention to deal with method or laboratory changes
suspected to impact data values, and representation of left- and
interval-censored data. The approach has been applied to water quality data
in the Chesapeake Bay, a major estuary on the east coast of the United
States to provide insights to a range of management- and research-focused
questions. Methodology described in Murphy (2019)
<doi:10.1016/j.envsoft.2019.03.027>.
Author: Rebecca Murphy, Elgin Perry, Jennifer Keisman, Jon Harcum, Erik W Leppo
Maintainer: Erik W Leppo <Erik.Leppo@tetratech.com>
Diff between baytrends versions 1.2.1 dated 2020-03-31 and 2.0.2 dated 2020-11-24
baytrends-1.2.1/baytrends/R/a1_smwrQW_qw-class.R |only baytrends-1.2.1/baytrends/R/a2_smwrQW_lcens-class.R |only baytrends-1.2.1/baytrends/R/a3_smwrQW_mcens-class.R |only baytrends-1.2.1/baytrends/R/as.lcens.R |only baytrends-1.2.1/baytrends/R/as.mcens.R |only baytrends-1.2.1/baytrends/R/as.qw.R |only baytrends-1.2.1/baytrends/R/qw.export.R |only baytrends-1.2.1/baytrends/R/qw.import.R |only baytrends-1.2.1/baytrends/R/smwrBase_group2row.R |only baytrends-1.2.1/baytrends/R/smwrBase_importRDB.R |only baytrends-1.2.1/baytrends/R/smwrBase_isLike.R |only baytrends-1.2.1/baytrends/R/smwrBase_z%cn%.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_addCaption.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_colorPlot.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_colors.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_datePretty.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_lineWt.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_linearPretty.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_logPretty.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_month.USGS.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_namePretty.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_numericData.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_refLine.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_renderPretty.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_setAxis.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_setColor.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_setExplan.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_setGD.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_setMargin.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_setMultiPlot.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_setPage.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_setPlot.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_strip.blanks.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_timePlot.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_timePretty.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_transData.R |only 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baytrends-2.0.2/baytrends/man/detrended.salinity.Rd | 256 ++--- baytrends-2.0.2/baytrends/man/dot-ExpLNiCens.Rd | 46 - baytrends-2.0.2/baytrends/man/dot-ExpLNlCens.Rd | 46 - baytrends-2.0.2/baytrends/man/dot-ExpLNmCens.Rd | 42 baytrends-2.0.2/baytrends/man/dot-ExpLNrCens.Rd | 46 - baytrends-2.0.2/baytrends/man/dot-ExpNiCens.Rd | 46 - baytrends-2.0.2/baytrends/man/dot-ExpNlCens.Rd | 46 - baytrends-2.0.2/baytrends/man/dot-ExpNmCens.Rd | 42 baytrends-2.0.2/baytrends/man/dot-ExpNrCens.Rd | 46 - baytrends-2.0.2/baytrends/man/dot-F.Rd | 64 - baytrends-2.0.2/baytrends/man/dot-H.Rd | 52 - baytrends-2.0.2/baytrends/man/dot-H1.Rd | 50 - baytrends-2.0.2/baytrends/man/dot-H2.Rd | 50 - baytrends-2.0.2/baytrends/man/dot-H3.Rd | 50 - baytrends-2.0.2/baytrends/man/dot-H4.Rd | 50 - baytrends-2.0.2/baytrends/man/dot-H5.Rd | 50 - baytrends-2.0.2/baytrends/man/dot-P.Rd | 48 - baytrends-2.0.2/baytrends/man/dot-T.Rd | 64 - baytrends-2.0.2/baytrends/man/dot-V.Rd | 58 - baytrends-2.0.2/baytrends/man/dot-appendDateFeatures.Rd | 56 - baytrends-2.0.2/baytrends/man/dot-checkRange.Rd | 120 +- baytrends-2.0.2/baytrends/man/dot-chkParameter.Rd | 50 - baytrends-2.0.2/baytrends/man/dot-findFile.Rd | 108 +- baytrends-2.0.2/baytrends/man/dot-fmtPval.Rd | 30 baytrends-2.0.2/baytrends/man/dot-gamANOVA.Rd | 30 baytrends-2.0.2/baytrends/man/dot-gamCoeff.Rd | 34 baytrends-2.0.2/baytrends/man/dot-gamDiffPORtbl.Rd | 34 baytrends-2.0.2/baytrends/man/dot-gamPlotCalc.Rd | 100 +- baytrends-2.0.2/baytrends/man/dot-initializeResults.Rd | 28 baytrends-2.0.2/baytrends/man/dot-mergeFlow.Rd | 58 - baytrends-2.0.2/baytrends/man/dot-mergeSalinity.Rd | 46 - baytrends-2.0.2/baytrends/man/dot-reAttDF.Rd | 70 - baytrends-2.0.2/baytrends/man/dot-vTable.Rd | 34 baytrends-2.0.2/baytrends/man/eventProcessing.Rd | 128 +- baytrends-2.0.2/baytrends/man/fillMissing.Rd | 190 ++-- baytrends-2.0.2/baytrends/man/filterWgts.Rd | 60 - baytrends-2.0.2/baytrends/man/flwAveragePred.Rd | 44 - baytrends-2.0.2/baytrends/man/gamDiff.Rd | 212 ++-- baytrends-2.0.2/baytrends/man/gamPlotDisp.Rd | 116 +- baytrends-2.0.2/baytrends/man/gamPlotDispSeason.Rd | 192 ++-- baytrends-2.0.2/baytrends/man/gamTest.Rd | 316 +++---- baytrends-2.0.2/baytrends/man/gamTestSeason.Rd | 206 ++-- baytrends-2.0.2/baytrends/man/getUSGSflow.Rd | 116 +- baytrends-2.0.2/baytrends/man/impute.Rd | 76 - baytrends-2.0.2/baytrends/man/imputeDF.Rd |only baytrends-2.0.2/baytrends/man/layerAggregation.Rd |only baytrends-2.0.2/baytrends/man/layerLukup.Rd | 44 - baytrends-2.0.2/baytrends/man/loadData.Rd | 184 ++-- baytrends-2.0.2/baytrends/man/loadExcel.Rd | 168 +-- baytrends-2.0.2/baytrends/man/loadModels.Rd | 72 - baytrends-2.0.2/baytrends/man/loadModelsResid.Rd | 36 baytrends-2.0.2/baytrends/man/makeSurvDF.Rd |only baytrends-2.0.2/baytrends/man/na2miss.Rd | 82 - baytrends-2.0.2/baytrends/man/nobs.Rd |only baytrends-2.0.2/baytrends/man/parameterList.Rd | 70 - baytrends-2.0.2/baytrends/man/sal.Rd | 44 - baytrends-2.0.2/baytrends/man/saveDF.Rd | 108 +- baytrends-2.0.2/baytrends/man/seasAdjflow.Rd | 124 +- baytrends-2.0.2/baytrends/man/selectData.Rd | 321 +++---- baytrends-2.0.2/baytrends/man/stationMasterList.Rd | 100 +- baytrends-2.0.2/baytrends/man/unSurv.Rd |only baytrends-2.0.2/baytrends/man/unSurvDF.Rd |only baytrends-2.0.2/baytrends/man/usgsGages.Rd | 40 baytrends-2.0.2/baytrends/tests |only baytrends-2.0.2/baytrends/vignettes/Detrending_Flow_and_Salinity_Data.Rmd |only baytrends-2.0.2/baytrends/vignettes/Processing_Censored_Data.Rmd |only baytrends-2.0.2/baytrends/vignettes/dataCensored.test.rda |binary baytrends-2.0.2/baytrends/vignettes/df1_2020_11_12_150309.csv |only baytrends-2.0.2/baytrends/vignettes/df1_2020_11_12_151819.csv |only baytrends-2.0.2/baytrends/vignettes/df1_2020_11_12_152418.csv |only baytrends-2.0.2/baytrends/vignettes/df1_2020_11_12_154129.csv |only baytrends-2.0.2/baytrends/vignettes/df1_2020_11_18_092151.csv |only baytrends-2.0.2/baytrends/vignettes/df1_2020_11_18_092816.csv |only baytrends-2.0.2/baytrends/vignettes/df1_2020_11_20_085603.csv |only baytrends-2.0.2/baytrends/vignettes/test.Rmd |only baytrends-2.0.2/baytrends/vignettes/wf_example_csv_file.PNG |only baytrends-2.0.2/baytrends/vignettes/wf_example_csv_file_small.PNG |only baytrends-2.0.2/baytrends/vignettes/wf_example_dataframe.PNG |only baytrends-2.0.2/baytrends/vignettes/wf_example_dataframe_small.PNG |only baytrends-2.0.2/baytrends/vignettes/wf_workflow.PNG |only baytrends-2.0.2/baytrends/vignettes/wf_workflow_small.PNG |only 339 files changed, 4521 insertions(+), 4279 deletions(-)
Title: Fast Computation of some Matrices Useful in Statistics
Description: Small set of functions to fast computation of some matrices and operations
useful in statistics.
Author: Felipe Osorio [aut, cre] (<https://orcid.org/0000-0002-4675-5201>),
Alonso Ogueda [aut]
Maintainer: Felipe Osorio <felipe.osorios@usm.cl>
Diff between fastmatrix versions 0.2-3571 dated 2020-10-10 and 0.3 dated 2020-11-24
fastmatrix-0.2-3571/fastmatrix/src/cpy_triangle.f |only fastmatrix-0.2-3571/fastmatrix/src/stats.c |only fastmatrix-0.3/fastmatrix/ChangeLog | 72 ++-- fastmatrix-0.3/fastmatrix/DESCRIPTION | 8 fastmatrix-0.3/fastmatrix/MD5 | 54 +-- fastmatrix-0.3/fastmatrix/NAMESPACE | 10 fastmatrix-0.3/fastmatrix/R/cholesky.R |only fastmatrix-0.3/fastmatrix/R/cov.R | 4 fastmatrix-0.3/fastmatrix/R/lu.R | 8 fastmatrix-0.3/fastmatrix/R/mahalanobis.R |only fastmatrix-0.3/fastmatrix/R/mardia.R |only fastmatrix-0.3/fastmatrix/R/norms.R | 4 fastmatrix-0.3/fastmatrix/R/ols.R | 6 fastmatrix-0.3/fastmatrix/R/sherman_morrison.R | 11 fastmatrix-0.3/fastmatrix/R/tri_mat.R |only fastmatrix-0.3/fastmatrix/inst/CITATION | 4 fastmatrix-0.3/fastmatrix/inst/include/fastmatrix.h | 34 + fastmatrix-0.3/fastmatrix/inst/include/fastmatrix_API.h | 188 ++++++++++ fastmatrix-0.3/fastmatrix/man/Mahalanobis.Rd |only fastmatrix-0.3/fastmatrix/man/cov.MSSD.Rd | 6 fastmatrix-0.3/fastmatrix/man/cov.weighted.Rd | 12 fastmatrix-0.3/fastmatrix/man/is.lower.tri.Rd |only fastmatrix-0.3/fastmatrix/man/kurtosis.Rd |only fastmatrix-0.3/fastmatrix/src/R_init_fastmatrix.c | 213 ++++++------ fastmatrix-0.3/fastmatrix/src/distance_API.c |only fastmatrix-0.3/fastmatrix/src/fastmatrix.h | 44 ++ fastmatrix-0.3/fastmatrix/src/ls_API.c |only fastmatrix-0.3/fastmatrix/src/mahalanobis.c |only fastmatrix-0.3/fastmatrix/src/mardia.c |only fastmatrix-0.3/fastmatrix/src/matrix_API.c | 284 +++++++++++++++- fastmatrix-0.3/fastmatrix/src/ols.c | 2 fastmatrix-0.3/fastmatrix/src/power_method.c | 6 fastmatrix-0.3/fastmatrix/src/sherman_morrison.c | 35 + fastmatrix-0.3/fastmatrix/src/stats_API.c |only fastmatrix-0.3/fastmatrix/src/utils.c | 24 - 35 files changed, 791 insertions(+), 238 deletions(-)
Title: Gaussian Process Models for Scalar and Functional Inputs
Description: Construction and smart selection of Gaussian process models
with emphasis on treatment of functional inputs. This package
offers: (i) flexible modeling of functional-input regression
problems through the fairly general Gaussian process model; (ii)
built-in dimension reduction for functional inputs; (iii)
heuristic optimization of the structural parameters of the model
(e.g., active inputs, kernel function, type of distance).
Metamodeling background is provided in
Betancourt et al. (2020) <doi:10.1016/j.ress.2020.106870>.
The algorithm for structural parameter optimization is described
in <https://hal.archives-ouvertes.fr/hal-02532713>.
Author: Jose Betancourt [cre, aut],
François Bachoc [aut],
Thierry Klein [aut],
Deborah Idier [ctb],
Jeremy Rohmer [ctb]
Maintainer: Jose Betancourt <djbetancourt@uninorte.edu.co>
Diff between funGp versions 0.2.0 dated 2020-11-17 and 0.2.1 dated 2020-11-24
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 9 +++++++-- R/3_ant_admin.R | 3 +-- man/get_active_in.Rd | 3 +-- 5 files changed, 17 insertions(+), 14 deletions(-)
Title: Manage Competition Results
Description: Tools for storing and managing competition results.
Competition is understood as a set of games in which players gain some
abstract scores. There are two ways for storing results: in long (one
row per game-player) and wide (one row per game with fixed amount of
players) formats. This package provides functions for creation and
conversion between them. Also there are functions for computing their
summary and Head-to-Head values for players. They leverage grammar of
data manipulation from 'dplyr'.
Author: Evgeni Chasnovski [aut, cre] (<https://orcid.org/0000-0002-1617-4019>)
Maintainer: Evgeni Chasnovski <evgeni.chasnovski@gmail.com>
Diff between comperes versions 0.2.4 dated 2020-05-09 and 0.2.5 dated 2020-11-23
DESCRIPTION | 13 MD5 | 78 +- NEWS.md | 4 R/comperes-package.R | 2 R/head-to-head.R | 14 R/item-summary.R | 3 R/outer-methods.R | 4 R/pair-value-data.R | 4 R/pairgames.R | 1 R/results-longcr.R | 16 R/results-widecr.R | 26 R/utils-pipe.R | 2 R/utils.R | 8 R/zzz.R | 4 README.md | 73 +- build/vignette.rds |binary inst/doc/formats.html | 702 ++++++++++-------------- inst/doc/manipulation.html | 961 +++++++++++++++------------------- man/comperes-package.Rd | 6 man/convert-pair-value.Rd | 1 man/get_matchups.Rd | 1 man/h2h_funs.Rd | 5 man/h2h_long.Rd | 1 man/h2h_mat.Rd | 1 man/item-summary-join.Rd | 3 man/item-summary.Rd | 1 man/levels2.Rd | 1 man/longcr.Rd | 1 man/pairgames.Rd | 1 man/pipe.Rd | 2 man/summary_funs.Rd | 5 man/widecr.Rd | 3 tests/testthat/test-head-to-head.R | 21 tests/testthat/test-item-summary.R | 24 tests/testthat/test-outer-methods.R | 28 tests/testthat/test-pair-value-data.R | 16 tests/testthat/test-pairgames.R | 4 tests/testthat/test-results-longcr.R | 118 ++-- tests/testthat/test-results-widecr.R | 129 +++- tests/testthat/test-utils.R | 36 - 40 files changed, 1157 insertions(+), 1166 deletions(-)
Title: Calculate Second-Generation p-Values and Associated Measures
Description: Computation of second-generation p-values as described in Blume et al. (2018) <doi:10.1371/journal.pone.0188299> and Blume et al. (2019) <doi:10.1080/00031305.2018.1537893>. There are additional functions which provide power and type I error calculations, create graphs (particularly suited for large-scale inference usage), and a function to estimate false discovery rates based on second-generation p-value inference.
Author: Valerie Welty [aut, cre],
Rebecca Irlmeier [aut],
Thomas Stewart [aut],
Robert Greevy, Jr. [aut],
Lucy D'Agostino McGowan [aut],
Jeffrey Blume [aut]
Maintainer: Valerie Welty <valerie.welty@vanderbilt.edu>
Diff between sgpv versions 1.0.0 dated 2020-07-06 and 1.1.0 dated 2020-11-23
DESCRIPTION | 10 ++++++---- MD5 | 14 +++++++++----- NAMESPACE | 7 +++++++ R/fdrisk.R | 2 +- R/plotman.R |only R/plotsgpower.R |only README.md | 15 ++++++++++++--- man/fdrisk.Rd | 2 +- man/plotman.Rd |only man/plotsgpower.Rd |only 10 files changed, 36 insertions(+), 14 deletions(-)
Title: High Performance Algorithms for Vine Copula Modeling
Description: Provides an interface to 'vinecopulib', a C++ library for vine
copula modeling. The 'rvinecopulib' package implements the core features of the
popular 'VineCopula' package, in particular inference algorithms for both vine
copula and bivariate copula models. Advantages over 'VineCopula' are a sleeker
and more modern API, improved performances, especially in high dimensions,
nonparametric and multi-parameter families, and the ability to model discrete
variables. The 'rvinecopulib' package includes 'vinecopulib' as header-only
C++ library (currently version 0.5.5). Thus users do not need to install
'vinecopulib' itself in order to use 'rvinecopulib'. Since their initial
releases, 'vinecopulib' is licensed under the MIT License, and 'rvinecopulib'
is licensed under the GNU GPL version 3.
Author: Thomas Nagler [aut, cre],
Thibault Vatter [aut]
Maintainer: Thomas Nagler <info@vinecopulib.org>
Diff between rvinecopulib versions 0.5.4.1.0 dated 2020-10-03 and 0.5.5.1.0 dated 2020-11-23
DESCRIPTION | 8 +- MD5 | 22 ++--- NEWS.md | 19 +++++ R/rvinecopulib.R | 2 inst/include/vinecopulib/bicop/class.hpp | 2 inst/include/vinecopulib/bicop/implementation/bb7.ipp | 12 +-- inst/include/vinecopulib/bicop/implementation/class.ipp | 13 ++- inst/include/vinecopulib/vinecop/implementation/class.ipp | 2 inst/include/vinecopulib/vinecop/implementation/fit_controls.ipp | 6 - inst/include/vinecopulib/vinecop/implementation/tools_select.ipp | 37 +++------- man/rvinecopulib.Rd | 2 tests/testthat/Rplots.pdf |binary 12 files changed, 66 insertions(+), 59 deletions(-)
Title: MCMC, Particle Filtering, and Programmable Hierarchical Modeling
Description: A system for writing hierarchical statistical models largely
compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models
and do basic R-style math, and compiling both models and nimbleFunctions via
custom-generated C++. 'NIMBLE' includes default methods for MCMC, Monte Carlo
Expectation Maximization, and some other tools. The nimbleFunction system makes
it easy to do things like implement new MCMC samplers from R, customize the
assignment of samplers to different parts of a model from R, and compile the
new samplers automatically via C++ alongside the samplers 'NIMBLE' provides.
'NIMBLE' extends the 'BUGS'/'JAGS' language by making it extensible: New
distributions and functions can be added, including as calls to external
compiled code. Although most people think of MCMC as the main goal of the
'BUGS'/'JAGS' language for writing models, one can use 'NIMBLE' for writing
arbitrary other kinds of model-generic algorithms as well. A full User Manual is
available at <https://r-nimble.org>.
Author: Perry de Valpine [aut],
Christopher Paciorek [aut, cre],
Daniel Turek [aut],
Nick Michaud [aut],
Cliff Anderson-Bergman [aut],
Fritz Obermeyer [aut],
Claudia Wehrhahn Cortes [aut] (Bayesian nonparametrics system),
Abel Rodrìguez [aut] (Bayesian nonparametrics system),
Duncan Temple Lang [aut] (packaging configuration),
Sally Paganin [aut] (reversible jump MCMC),
Jagadish Babu [ctb] (code for the compilation system for an early
version of NIMBLE),
Lauren Ponisio [ctb] (contributions to the cross-validation code),
Peter Sujan [ctb] (multivariate t distribution code)
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Diff between nimble versions 0.10.0 dated 2020-10-10 and 0.10.1 dated 2020-11-23
nimble-0.10.0/nimble/man/samplerAssignmentRules-class.Rd |only nimble-0.10.1/nimble/DESCRIPTION | 8 nimble-0.10.1/nimble/INSTALL | 6 nimble-0.10.1/nimble/MD5 | 52 - nimble-0.10.1/nimble/NAMESPACE | 3 nimble-0.10.1/nimble/R/BNP_samplers.R | 26 nimble-0.10.1/nimble/R/BUGS_model.R | 30 + nimble-0.10.1/nimble/R/BUGS_readBUGS.R | 2 nimble-0.10.1/nimble/R/MCMC_autoBlock.R | 3 nimble-0.10.1/nimble/R/MCMC_build.R | 48 - nimble-0.10.1/nimble/R/MCMC_configuration.R | 394 ++------------ nimble-0.10.1/nimble/R/MCMC_utils.R | 43 + nimble-0.10.1/nimble/R/nimbleFunction_Rexecution.R | 11 nimble-0.10.1/nimble/R/nimbleFunction_keywordProcessing.R | 7 nimble-0.10.1/nimble/R/options.R | 5 nimble-0.10.1/nimble/inst/NEWS | 20 nimble-0.10.1/nimble/inst/tests/mcmcTestLog_Correct.Rout | 12 nimble-0.10.1/nimble/inst/tests/test-getDependencies.R | 33 + nimble-0.10.1/nimble/inst/tests/test-getParam.R | 117 ++++ nimble-0.10.1/nimble/inst/tests/test-mcmc.R | 53 + nimble-0.10.1/nimble/inst/tests/test-waic.R | 50 - nimble-0.10.1/nimble/man/MCMCconf-class.Rd | 2 nimble-0.10.1/nimble/man/autoBlock.Rd | 4 nimble-0.10.1/nimble/man/buildMCMC.Rd | 42 - nimble-0.10.1/nimble/man/configureMCMC.Rd | 7 nimble-0.10.1/nimble/man/makeParamInfo.Rd | 4 nimble-0.10.1/nimble/man/modelInitialization.Rd |only nimble-0.10.1/nimble/man/nimble-internal.Rd | 49 + 28 files changed, 538 insertions(+), 493 deletions(-)
Title: Coloring Wildlife Distributions in Space-Time
Description: Color and visualize wildlife distributions in
space-time using raster data. In addition to enabling display of
sequential change in distributions through the use of small multiples,
'colorist' provides functions for extracting several features of
interest from a sequence of distributions and for visualizing those
features using HCL (hue-chroma-luminance) color palettes. Resulting
maps allow for "fair" visual comparison of intensity values (e.g.,
occurrence, abundance, or density) across space and time and can be
used to address questions about where, when, and how consistently a
species, group, or individual is likely to be found.
Author: Justin Schuetz [aut] (<https://orcid.org/0000-0002-6163-538X>),
Matthew Strimas-Mackey [aut, cre]
(<https://orcid.org/0000-0001-8929-7776>),
Tom Auer [aut] (<https://orcid.org/0000-0001-8619-7147>)
Maintainer: Matthew Strimas-Mackey <mes335@cornell.edu>
Diff between colorist versions 0.1.1 dated 2020-08-13 and 0.1.2 dated 2020-11-23
DESCRIPTION | 11 MD5 | 44 ++- NEWS.md | 6 R/legend.R | 173 +++++++++----- R/map.R | 94 ++++++- R/palette.R | 12 - README.md | 15 - build/vignette.rds |binary inst/doc/introduction.R | 1 inst/doc/introduction.Rmd | 11 inst/doc/introduction.html | 382 ++++++++++++++++++-------------- inst/doc/mapping.R |only inst/doc/mapping.Rmd |only inst/doc/mapping.html |only inst/doc/tuning.Rmd | 2 inst/doc/tuning.html | 207 +++++++++++------ man/legend_set.Rd | 25 +- man/legend_timecycle.Rd | 12 + man/legend_timeline.Rd | 16 + man/map_multiples.Rd | 23 + man/map_single.Rd | 41 ++- vignettes/introduction.Rmd | 11 vignettes/mapping.Rmd |only vignettes/qgis-screenshot-default.png |only vignettes/qgis-screenshot-symbology.png |only vignettes/tuning.Rmd | 2 26 files changed, 715 insertions(+), 373 deletions(-)