Title: A Method to Download Department of Education College Scorecard
Data
Description: A method to download Department of Education College
Scorecard data using the public API
<https://collegescorecard.ed.gov/data/documentation/>. It is based on
the 'dplyr' model of piped commands to select and filter data in a
single chained function call. An API key from the U.S. Department of
Education is required.
Author: Benjamin Skinner [aut, cre] (<https://orcid.org/0000-0002-0337-7415>)
Maintainer: Benjamin Skinner <btskinner@virginia.edu>
Diff between rscorecard versions 0.11.1 dated 2018-11-05 and 0.12.0 dated 2019-05-21
rscorecard-0.11.1/rscorecard/tests/testthat/helper.R |only rscorecard-0.12.0/rscorecard/DESCRIPTION | 8 ++++---- rscorecard-0.12.0/rscorecard/MD5 | 6 +++--- rscorecard-0.12.0/rscorecard/R/sysdata.rda |binary rscorecard-0.12.0/rscorecard/tests/testthat/helper-xyz.R |only 5 files changed, 7 insertions(+), 7 deletions(-)
Title: Prepare MCMCtree Analyses and Plot Bayesian Divergence Time
Analyses Estimates on Trees
Description: Provides functions to prepare time priors for 'MCMCtree' analyses in the 'PAML' software from Yang (2007)<doi:10.1093/molbev/msm088> and plot time-scaled phylogenies from any Bayesian divergence time analysis. Most time-calibrated node prior distributions require user-specified parameters. The package provides functions to refine these parameters, so that the resulting prior distributions accurately reflect confidence in known, usually fossil, time information. These functions also enable users to visualise distributions and write 'MCMCtree' ready input files. Additionally, the package supplies flexible functions to visualise age uncertainty on a plotted tree with using node bars, using branch widths proportional to the age uncertainty, or by plotting the full posterior distributions on nodes. Time-scaled phylogenetic plots can be visualised with absolute and geological timescales . All plotting functions are applicable with output from any Bayesian software, not just 'MCMCtree'.
Author: Mark Puttick [aut,cre], Pascal Title [ctb]
Maintainer: Mark Puttick <mark.puttick@bristol.ac.uk>
Diff between MCMCtreeR versions 1.0 dated 2019-05-20 and 1.1 dated 2019-05-21
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/doc/MCMCtree.html | 4 ++-- inst/doc/MCMCtree_plot.html | 6 +++--- 4 files changed, 12 insertions(+), 12 deletions(-)
Title: Bayesian Structural Time Series
Description: Time series regression using dynamic linear models fit using
MCMC. See Scott and Varian (2014) <DOI:10.1504/IJMMNO.2014.059942>, among many
other sources.
Author: Steven L. Scott <steve.the.bayesian@gmail.com>
Maintainer: Steven L. Scott <steve.the.bayesian@gmail.com>
Diff between bsts versions 0.8.0 dated 2018-05-07 and 0.9.0 dated 2019-05-21
DESCRIPTION | 12 MD5 | 128 ++- NAMESPACE | 14 R/add.dynamic.regression.R | 68 + R/add.local.level.R | 137 +++ R/add.regression.holiday.R | 9 R/bsts.R | 2 R/diagnostics.R | 25 R/dirm.R |only R/format.prediction.data.R | 75 +- R/format.timestamps.R | 10 R/holiday.R | 7 R/mbsts.R |only R/mbsts.plots.R |only R/plots.R | 6 R/predict.bsts.R | 404 +++++++++++ R/predict.mbsts.R |only R/utils.R | 132 +++ data/gdp.RData |only inst/tests/tests/testthat/test-dirm.R |only inst/tests/tests/testthat/test-dynamic-regression.R |only inst/tests/tests/testthat/test-holidays.R |only inst/tests/tests/testthat/test-multivariate.R |only inst/tests/tests/testthat/test-prediction-errors.R |only inst/tests/tests/testthat/test-prediction.R |only inst/tests/tests/testthat/test-regressionholiday.R | 41 - inst/tests/testthat/test-dirm.R |only inst/tests/testthat/test-dynamic-regression.R |only inst/tests/testthat/test-holidays.R |only inst/tests/testthat/test-multivariate.R |only inst/tests/testthat/test-prediction-errors.R |only inst/tests/testthat/test-prediction.R |only inst/tests/testthat/test-regressionholiday.R | 41 - man/add.dynamic.regression.Rd | 44 - man/add.local.level.Rd | 1 man/add.monthly.annual.cycle.Rd | 2 man/add.shared.local.level.Rd |only man/bsts.Rd | 8 man/compare.bsts.models.Rd | 4 man/dirm-model-options.Rd |only man/dirm.Rd |only man/gdp.Rd |only man/mixed.frequency.Rd | 2 man/one.step.prediction.errors.Rd | 12 man/predict.bsts.Rd | 57 + man/regularize.timestamps.Rd | 1 man/wide.to.long.Rd |only src/aggregate_time_series.cc | 2 src/bsts.cc | 115 +-- src/bsts_init.cc | 33 src/create_dynamic_intercept_state_model.cpp |only src/create_dynamic_intercept_state_model.h |only src/create_shared_state_model.cpp |only src/create_shared_state_model.h |only src/create_state_model.cpp |only src/create_state_model.h |only src/dirm.cc |only src/dynamic_intercept_model_manager.cc |only src/dynamic_intercept_model_manager.h |only src/get_date_ranges.cc | 5 src/mbsts.cc |only src/mixed_frequency.cc | 35 - src/model_manager.cc | 237 ++++-- src/model_manager.h | 699 +++++++++++--------- src/multivariate_gaussian_model_manager.cc |only src/multivariate_gaussian_model_manager.h |only src/state_space_gaussian_model_manager.cc | 14 src/state_space_gaussian_model_manager.h | 8 src/state_space_logit_model_manager.cc | 2 src/state_space_logit_model_manager.h | 7 src/state_space_poisson_model_manager.cc | 2 src/state_space_poisson_model_manager.h | 7 src/state_space_regression_model_manager.cc | 543 +++++++-------- src/state_space_regression_model_manager.h | 14 src/state_space_student_model_manager.cc | 5 src/state_space_student_model_manager.h | 172 ++-- src/utils.cc | 93 +- src/utils.h | 290 ++++---- tests/testthat/test-dirm.R |only tests/testthat/test-dynamic-regression.R |only tests/testthat/test-holidays.R |only tests/testthat/test-multivariate.R |only tests/testthat/test-prediction-errors.R |only tests/testthat/test-prediction.R |only tests/testthat/test-seasonal.R | 164 ++-- 85 files changed, 2442 insertions(+), 1247 deletions(-)
Title: Robust Methods for Epistasis Detection
Description: Functions to perform robust epistasis detection in genome-wide
association studies, as described in Slim et al. (2018) <doi:10.1101/442749>.
The implemented methods identify pairwise interactions between a particular
target variant and the rest of the genotype, using a propensity score
approach. The propensity score models the linkage disequilibrium between the
target and the rest of the genotype. All methods are penalized regression
approaches, which differently incorporate the propensity score to only
recover the synergistic effects between the target and the genotype.
Author: Lotfi Slim [aut, cre],
Clément Chatelain [ctb],
Chloé-Agathe Azencott [ctb],
Jean-Philippe Vert [ctb]
Maintainer: Lotfi Slim <lotfi.slim@mines-paristech.fr>
Diff between epiGWAS versions 1.0.0 dated 2018-12-16 and 1.0.1 dated 2019-05-21
DESCRIPTION | 6 +-- MD5 | 22 +++++++------- NEWS.md | 3 + R/forward.R | 13 ++++---- R/genotypes_data.R | 2 - R/methods.R | 2 - README.md | 51 +++++++++++++++++++++++---------- build/vignette.rds |binary inst/doc/epistasis.html | 74 +++++++++++++++++++++++++++++++++++------------- man/fast_HMM.Rd | 2 - man/genotypes.Rd | 2 - man/shifted_outcome.Rd | 2 - 12 files changed, 119 insertions(+), 60 deletions(-)
Title: Y&R Miscellaneous R Functions
Description: Miscellaneous functions for data analysis, portfolio management, graphics, data manipulation, statistical investigation, including descriptive statistics, creating leading and lagging variables, portfolio return analysis, time series difference and percentage change calculation, stacking data for higher efficient analysis.
Author: Manuel Russon <RUSSONM@stjohns.edu>, Xuanhua (Peter) Yin <peteryin.sju@hotmail.com>
Maintainer: Xuanhua (Peter) Yin <peteryin.sju@hotmail.com>
Diff between YRmisc versions 0.1.4 dated 2019-04-11 and 0.1.5 dated 2019-05-21
DESCRIPTION | 6 - MD5 | 172 +++++++++++++++++---------------- NAMESPACE | 1 NEWS | 244 +++++++++++++++++++++++++---------------------- R/pl.mv.R |only R/pt.bias.R |only R/pt.dalpha.R |only R/pt.dbeta.R |only R/pt.hismv.R |only R/pt.roy.R |only man/cor.lag.Rd | 50 ++++----- man/cor.spearman.Rd | 38 +++---- man/cv.annu.fv.Rd | 46 ++++---- man/cv.annu.pv.Rd | 46 ++++---- man/cv.axp.Rd | 46 ++++---- man/cv.bondprice.Rd | 50 ++++----- man/cv.diff.Rd | 40 +++---- man/cv.drawdown.Rd | 40 +++---- man/cv.lag.Rd | 42 ++++---- man/cv.lead.Rd | 42 ++++---- man/cv.logs.Rd | 46 ++++---- man/cv.pctcng.Rd | 38 +++---- man/cv.powers.Rd | 46 ++++---- man/df.sortcol.Rd | 42 ++++---- man/df.stack.Rd | 52 +++++----- man/ds.corm.Rd | 38 +++---- man/ds.kurt.Rd | 34 +++--- man/ds.skew.Rd | 38 +++---- man/ds.summ.Rd | 42 ++++---- man/pkg.reinstall.Rd | 38 +++---- man/pkg.save.Rd | 36 +++--- man/pl.2ts.Rd | 46 ++++---- man/pl.2tsgg.Rd | 54 +++++----- man/pl.3smoothtxt.Rd | 46 ++++---- man/pl.3smoothtxtgg.Rd | 58 +++++------ man/pl.3txt.Rd | 48 ++++----- man/pl.3txtgg.Rd | 60 +++++------ man/pl.coplot.Rd | 46 ++++---- man/pl.hist.Rd | 38 +++---- man/pl.histgg.Rd | 42 ++++---- man/pl.hs.Rd | 50 ++++----- man/pl.hsd.Rd | 38 +++---- man/pl.hsdgg.Rd | 42 ++++---- man/pl.mv.Rd |only man/pl.s.Rd | 42 ++++---- man/pl.sgg.Rd | 42 ++++---- man/pl.sm.Rd | 42 ++++---- man/pl.smgg.Rd | 48 ++++----- man/pl.ts.Rd | 38 +++---- man/pl.tsgg.Rd | 38 +++---- man/pl.tss.Rd | 42 ++++---- man/pt.alpha.Rd | 46 ++++---- man/pt.annexrtn.Rd | 46 ++++---- man/pt.annrtn.Rd | 40 +++---- man/pt.annsd.Rd | 44 ++++---- man/pt.beta.Rd | 46 ++++---- man/pt.bias.Rd |only man/pt.btavg.Rd | 44 ++++---- man/pt.cmexrtn.Rd | 44 ++++---- man/pt.cmrtn.Rd | 36 +++--- man/pt.dalpha.Rd |only man/pt.dbeta.Rd |only man/pt.exploss.Rd | 42 ++++---- man/pt.hismv.Rd |only man/pt.info.Rd | 50 ++++----- man/pt.jalpha.Rd | 58 +++++------ man/pt.m2.Rd | 50 ++++----- man/pt.probloss.Rd | 42 ++++---- man/pt.roy.Rd |only man/pt.sdexrtn.Rd | 44 ++++---- man/pt.semivar.Rd | 42 ++++---- man/pt.sharp.Rd | 56 +++++----- man/pt.sortino.Rd | 50 ++++----- man/pt.te.Rd | 44 ++++---- man/pt.treynor.Rd | 52 +++++----- man/pt.udrtn.Rd | 36 +++--- man/pt.updwcap.Rd | 48 ++++----- man/reg.adj.r.squared.Rd | 58 +++++------ man/reg.aic.Rd | 48 ++++----- man/reg.bic.Rd | 48 ++++----- man/reg.dof.Rd | 42 ++++---- man/reg.dw.Rd | 36 +++--- man/reg.linreg.Rd | 42 ++++---- man/reg.model.Rd | 38 +++---- man/reg.r.squared.Rd | 52 +++++----- man/reg.std.err.Rd | 50 ++++----- man/tr.log.Rd | 50 ++++----- man/tr.logtb.Rd | 50 ++++----- man/tr.nd.Rd | 42 ++++---- man/tr.unli.Rd | 42 ++++---- man/xd.avt.Rd | 64 ++++++------ man/xd.fred.Rd | 64 ++++++------ man/xd.fred.tickers.Rd | 28 ++--- 93 files changed, 1959 insertions(+), 1928 deletions(-)
Title: Load Data from Facebook API Marketing
Description: Load data by campaigns, ads, ad sets and insights, ad account and business manager from Facebook Marketing API into R. For more details see official documents by Facebook Marketing API <https://developers.facebook.com/docs/marketing-apis/>.
Author: Alexey Seleznev <selesnow@gmail.com>
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rfacebookstat versions 1.8.3 dated 2018-08-14 and 1.9.0 dated 2019-05-21
DESCRIPTION | 20 +- MD5 | 79 ++++++---- NAMESPACE | 33 +++- NEWS.md |only R/fbAPILimitCheck.R |only R/fbActions.R |only R/fbDeleteAdAccountUsers.R | 5 R/fbGetAdAccountUsers.R | 72 +++++---- R/fbGetAdAccountUsersPermissions.R | 6 R/fbGetAdAccounts.R | 6 R/fbGetAdCreative.R | 118 ++++++++------- R/fbGetAdSets.R | 10 - R/fbGetAds.R | 10 - R/fbGetApps.R | 4 R/fbGetBusinessManagers.R | 3 R/fbGetCampaigns.R | 10 - R/fbGetCatalogs.R |only R/fbGetLongTimeToken.R | 6 R/fbGetMarketingStat.R | 251 ++++++++++++++++++++++++---------- R/fbGetPages.R | 4 R/fbGetProjects.R | 4 R/fbGetToken.R | 3 R/fbUpdateAdAccountUsers.R | 6 R/zzz.R | 15 ++ README.md |only build/partial.rdb |binary build/vignette.rds |only inst |only man/fbDeleteAdAccountUsers.Rd | 9 - man/fbGetAdAccountUsers.Rd | 14 + man/fbGetAdAccountUsersPermissions.Rd | 7 man/fbGetAdAccounts.Rd | 6 man/fbGetAdCreative.Rd | 10 - man/fbGetAdSets.Rd | 8 - man/fbGetAds.Rd | 9 - man/fbGetApps.Rd | 9 - man/fbGetBusinessManagers.Rd | 3 man/fbGetCampaigns.Rd | 11 - man/fbGetCatalogs.Rd |only man/fbGetMarketingStat.Rd | 131 +++++++++++++++-- man/fbGetPages.Rd | 4 man/fbGetProjects.Rd | 5 man/fbUpdateAdAccountUsers.Rd | 11 - vignettes |only 44 files changed, 590 insertions(+), 312 deletions(-)
Title: Qualitative Comparative Analysis
Description: An extensive set of functions to perform Qualitative Comparative Analysis:
crisp sets ('csQCA'), temporal ('tQCA'), multi-value ('mvQCA')
and fuzzy sets ('fsQCA'), using a GUI - graphical user interface.
'QCA' is a methodology that bridges the qualitative and quantitative divide
in social science research. It uses a Boolean algorithm that results in a
minimal causal combination that explains a given phenomenon.
Author: Adrian Dusa [aut, cre, cph],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/gui/www/shared/jquery-AUTHORS.txt),
Vasil Dinkov [ctb, cph] (jquery.smartmenus.js library),
Dmitry Baranovskiy [ctb, cph] (raphael.js library),
Emmanuel Quentin [ctb, cph] (raphael.inline_text_editing.js library),
Jimmy Breck-McKye [ctb, cph] (raphael-paragraph.js library),
Alrik Thiem [aut] (from version 1.0-0 up to version 1.1-3)
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between QCA versions 3.4 dated 2019-01-18 and 3.5 dated 2019-05-21
QCA-3.4/QCA/R/combinations.R |only QCA-3.4/QCA/R/numeric.R |only QCA-3.4/QCA/R/prettyTable.R |only QCA-3.4/QCA/R/recode.R |only QCA-3.4/QCA/R/sortExpressions.R |only QCA-3.4/QCA/R/translate.R |only QCA-3.4/QCA/inst/gui/www/shared |only QCA-3.4/QCA/inst/staticdocs/XYplot-10.svgz |only QCA-3.4/QCA/inst/staticdocs/XYplot-11.svgz |only QCA-3.4/QCA/inst/staticdocs/XYplot-12.svgz |only QCA-3.4/QCA/inst/staticdocs/XYplot-13.svgz |only QCA-3.4/QCA/inst/staticdocs/XYplot-14.svgz |only QCA-3.4/QCA/inst/staticdocs/XYplot-15.svgz |only QCA-3.4/QCA/inst/staticdocs/XYplot-3.svgz |only QCA-3.4/QCA/inst/staticdocs/XYplot-5.svgz |only QCA-3.4/QCA/inst/staticdocs/XYplot-6.svgz |only QCA-3.4/QCA/inst/staticdocs/XYplot-7.svgz |only QCA-3.4/QCA/inst/staticdocs/XYplot-8.svgz |only QCA-3.4/QCA/inst/staticdocs/XYplot-9.svgz |only QCA-3.4/QCA/inst/staticdocs/Xplot-1.svgz |only QCA-3.4/QCA/inst/staticdocs/Xplot-2.svgz |only QCA-3.4/QCA/inst/staticdocs/Xplot-3.svgz |only QCA-3.4/QCA/inst/staticdocs/Xplot-4.svgz |only QCA-3.4/QCA/inst/staticdocs/calibrate-10.svgz |only QCA-3.4/QCA/inst/staticdocs/calibrate-12.svgz |only QCA-3.4/QCA/inst/staticdocs/calibrate-14.svgz |only QCA-3.4/QCA/inst/staticdocs/calibrate-16.svgz |only QCA-3.4/QCA/inst/staticdocs/calibrate-18.svgz |only QCA-3.4/QCA/inst/staticdocs/calibrate-20.svgz |only QCA-3.4/QCA/inst/staticdocs/calibrate-21.svgz |only QCA-3.4/QCA/inst/staticdocs/calibrate-22.svgz |only QCA-3.4/QCA/inst/staticdocs/calibrate-26.svgz |only QCA-3.4/QCA/inst/staticdocs/calibrate-3.svgz |only QCA-3.4/QCA/inst/staticdocs/calibrate-30.svgz |only QCA-3.4/QCA/inst/staticdocs/calibrate-31.svgz |only QCA-3.4/QCA/inst/staticdocs/calibrate-6.svgz |only QCA-3.4/QCA/inst/staticdocs/calibrate-8.svgz |only QCA-3.4/QCA/inst/staticdocs/minimize-1.svgz |only QCA-3.4/QCA/inst/staticdocs/minimize-2.svgz |only QCA-3.4/QCA/inst/staticdocs/subsetsAndSupersets-2.svgz |only QCA-3.4/QCA/inst/staticdocs/truthTable-20.svgz |only QCA-3.4/QCA/inst/staticdocs/truthTable-22.svgz |only QCA-3.4/QCA/man/recode.Rd |only QCA-3.5/QCA/DESCRIPTION | 11 QCA-3.5/QCA/MD5 | 316 ++-- QCA-3.5/QCA/NAMESPACE | 43 QCA-3.5/QCA/R/Electron.R | 8 QCA-3.5/QCA/R/XYplot.R | 34 QCA-3.5/QCA/R/calibrate.R | 10 QCA-3.5/QCA/R/causalChain.R | 5 QCA-3.5/QCA/R/combint.R |only QCA-3.5/QCA/R/compute.R | 12 QCA-3.5/QCA/R/createMatrix.R | 6 QCA-3.5/QCA/R/factorize.R | 82 - 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Title: An R Port of the 'ImageJ' Plugin 'Auto Threshold'
Description: Algorithms for automatically finding appropriate thresholds for
numerical data, with special functions for thresholding images. Provides the
'ImageJ' 'Auto Threshold' plugin functionality to R users. See
<http://imagej.net/Auto_Threshold> and Landini et al. (2017)
<DOI:10.1111/jmi.12474>.
Author: Rory Nolan [aut, cre, trl] (<https://orcid.org/0000-0002-5239-4043>),
Luis Alvarez [ctb] (<https://orcid.org/0000-0003-1316-1906>),
Sergi Padilla-Parra [ctb, ths]
(<https://orcid.org/0000-0002-8010-9481>),
Gabriel Landini [ctb, cph] (<https://orcid.org/0000-0002-9689-0989>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between autothresholdr versions 1.3.0 dated 2018-11-05 and 1.3.1 dated 2019-05-21
DESCRIPTION | 19 ++++++---- MD5 | 18 +++++----- NEWS.md | 7 +++ R/utils.R | 56 ------------------------------- build/vignette.rds |binary inst/WORDLIST |only inst/doc/finding-thresholds.html | 57 ++++++++++++++++++++++---------- inst/doc/thresholding-image-stacks.html | 41 +++++++++++++++++------ inst/doc/thresholding-images.html | 41 +++++++++++++++++------ tests/spelling.R |only tests/testthat/test_utils.R | 13 ------- 11 files changed, 132 insertions(+), 120 deletions(-)
More information about autothresholdr at CRAN
Permanent link
Title: Visualising Bipartite Networks and Calculating Some (Ecological)
Indices
Description: Functions to visualise webs and calculate a series of indices commonly used to describe pattern in (ecological) webs. It focuses on webs consisting of only two levels (bipartite), e.g. pollination webs or predator-prey-webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the web's topology.
Author: Carsten F. Dormann, Jochen Fruend and Bernd Gruber, with additional code from Stephen Beckett, Mariano Devoto, Jose Iriondo, Tove Opsahl, Rouven Strauss and Diego Vazquez, also based on C-code developed by Nils Bluethgen, Aaron Clauset/Rouven Strauss and Miguel Rodriguez-Girones
Maintainer: Carsten F. Dormann <carsten.dormann@biom.uni-freiburg.de>
Diff between bipartite versions 2.11 dated 2018-07-11 and 2.13 dated 2019-05-21
DESCRIPTION | 11 ++-- MD5 | 76 ++++++++++++++++++++++------- NAMESPACE | 10 +-- R/C.score.R | 84 ++++++++++++++++----------------- R/NOS.R | 57 +++++++++++----------- R/array2linkmx.R |only R/betalinkr.R |only R/betalinkr_multi.R |only R/decimalr2dtable.R |only R/empty.R | 80 +++++++++++++++---------------- R/nest.smdm.R |only R/networklevel.R | 1 R/nullmodel.r | 9 ++- R/specieslevel.R | 12 ++-- R/vaznullexternal.R |only R/webs2array.R | 20 +++++-- R/zzz.R | 8 --- build |only inst/doc/Dormann2008Rnews.pdf |binary inst/doc/Dormann2009OpenEcolJ.pdf |binary inst/doc/Dormann2011NetworkBiology.pdf |binary inst/doc/Intro2bipartite.R |only inst/doc/Intro2bipartite.Rnw |only inst/doc/Intro2bipartite.pdf |only man/NOS.Rd | 2 man/array2linkmx.Rd |only man/betalinkr.Rd |only man/bipartite-package.Rd | 33 +++++++++--- man/decimalr2dtable.Rd |only man/modulesLPA.Rd | 2 man/nest.smdm.Rd |only man/networklevel.Rd | 4 - man/r2dexternal.Rd | 13 +++-- man/webs2array.Rd | 9 ++- src/bmn5.cc | 6 +- vignettes |only 36 files changed, 256 insertions(+), 181 deletions(-)
Title: Amazon Redshift Tools
Description: Efficiently upload data into an Amazon Redshift database using the approach recommended by Amazon <https://aws.amazon.com/es/redshift/>.
Author: Pablo Seibelt [aut, cre]
Maintainer: Pablo Seibelt <pabloseibelt@sicarul.com>
Diff between redshiftTools versions 1.0.0 dated 2019-05-16 and 1.0.1 dated 2019-05-21
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 10 +++------- NEWS.md | 6 +++++- R/internal.R | 49 +++++++++++++++++++------------------------------ README.md | 9 +++++++-- 6 files changed, 43 insertions(+), 49 deletions(-)
Title: Provides Easy Downloading Capabilities for the UK Parliament API
Description: Provides functions to download data from the
<http://www.data.parliament.uk/> APIs. Because of the structure of the API,
there is a named function for each type of available data for ease of use,
as well as some functions designed to retrieve specific pieces of commonly
used data. Functions for each new API will be added as and when they become
available.
Author: Evan Odell [aut, cre] (<https://orcid.org/0000-0003-1845-808X>)
Maintainer: Evan Odell <evanodell91@gmail.com>
Diff between hansard versions 0.6.3 dated 2019-01-10 and 0.7.0 dated 2019-05-21
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hansard-0.7.0/hansard/tests/testthat-all1q.R | 8 hansard-0.7.0/hansard/tests/testthat-all2q.R | 8 hansard-0.7.0/hansard/tests/testthat-b.R | 8 hansard-0.7.0/hansard/tests/testthat-com.R | 8 hansard-0.7.0/hansard/tests/testthat-con.R | 8 hansard-0.7.0/hansard/tests/testthat-ea.R | 8 hansard-0.7.0/hansard/tests/testthat-election_candidates.R | 8 hansard-0.7.0/hansard/tests/testthat-election_results.R | 8 hansard-0.7.0/hansard/tests/testthat-elections.R | 8 hansard-0.7.0/hansard/tests/testthat-ep.R | 8 hansard-0.7.0/hansard/tests/testthat-lords1.R | 8 hansard-0.7.0/hansard/tests/testthat-lords2.R | 8 hansard-0.7.0/hansard/tests/testthat-mem.R | 8 hansard-0.7.0/hansard/tests/testthat-misc1.R | 8 hansard-0.7.0/hansard/tests/testthat-misc2.R | 8 hansard-0.7.0/hansard/tests/testthat-mp.R | 8 hansard-0.7.0/hansard/tests/testthat-r.R | 8 hansard-0.7.0/hansard/tests/testthat/test_1all_answered_questions.R | 71 hansard-0.7.0/hansard/tests/testthat/test_2all_answered_questions.R | 65 hansard-0.7.0/hansard/tests/testthat/test_bills.R | 75 hansard-0.7.0/hansard/tests/testthat/test_commons_functions.R | 204 - hansard-0.7.0/hansard/tests/testthat/test_constituencies.R | 25 hansard-0.7.0/hansard/tests/testthat/test_early_day_motions.R | 61 hansard-0.7.0/hansard/tests/testthat/test_election_candidates.R | 29 hansard-0.7.0/hansard/tests/testthat/test_election_results.R | 35 hansard-0.7.0/hansard/tests/testthat/test_elections.R | 87 hansard-0.7.0/hansard/tests/testthat/test_epetition.R | 71 hansard-0.7.0/hansard/tests/testthat/test_lords1.R | 103 hansard-0.7.0/hansard/tests/testthat/test_lords2.R | 143 - hansard-0.7.0/hansard/tests/testthat/test_members.R | 87 hansard-0.7.0/hansard/tests/testthat/test_misc1.R | 105 hansard-0.7.0/hansard/tests/testthat/test_misc2.R | 59 hansard-0.7.0/hansard/tests/testthat/test_mp_misc.R | 83 hansard-0.7.0/hansard/tests/testthat/test_research_briefings.R | 71 hansard-0.7.0/hansard/vignettes/introduction.Rmd | 548 ++-- 147 files changed, 11438 insertions(+), 11161 deletions(-)
Title: Tools for Analyzing Crossover Interference
Description: Analysis of crossover interference in experimental crosses,
particularly regarding the gamma model. See, for example,
Broman and Weber (2000) <doi:10.1086/302923>.
Author: Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>),
Il-Youp Kwak [ctb] (<https://orcid.org/0000-0002-7117-7669>)
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between xoi versions 0.67-4 dated 2018-03-08 and 0.68-3 dated 2019-05-21
xoi-0.67-4/xoi/R/zzz.R |only xoi-0.67-4/xoi/inst |only xoi-0.68-3/xoi/ChangeLog |only xoi-0.68-3/xoi/DESCRIPTION | 24 ++- xoi-0.68-3/xoi/MD5 | 90 ++++++------ xoi-0.68-3/xoi/R/bssbsb-data.R | 8 - xoi-0.68-3/xoi/R/chiasma.R | 21 +- xoi-0.68-3/xoi/R/coi_um.R | 15 +- xoi-0.68-3/xoi/R/coincidence.R | 11 - xoi-0.68-3/xoi/R/fitGamma.R | 57 ++++--- xoi-0.68-3/xoi/R/fitStahl.R | 33 ++-- xoi-0.68-3/xoi/R/gammaDensities.R | 221 +++++++++++++++---------------- xoi-0.68-3/xoi/R/kfunc.R | 5 xoi-0.68-3/xoi/R/kwak_coincidence.R | 8 - xoi-0.68-3/xoi/R/kwak_intensity.R | 8 - xoi-0.68-3/xoi/R/recrate.R | 19 +- xoi-0.68-3/xoi/R/simStahl.R | 17 +- xoi-0.68-3/xoi/R/util.R | 38 ++--- xoi-0.68-3/xoi/R/xoiversion.R | 2 xoi-0.68-3/xoi/data/bssbsb.RData |binary xoi-0.68-3/xoi/man/bssbsb.Rd | 6 xoi-0.68-3/xoi/man/chiasma.Rd | 22 +-- xoi-0.68-3/xoi/man/coincidence.Rd | 4 xoi-0.68-3/xoi/man/convertxoloc.Rd | 8 - xoi-0.68-3/xoi/man/countxo.Rd | 6 xoi-0.68-3/xoi/man/distance.given.two.Rd | 18 +- xoi-0.68-3/xoi/man/est.coi.Rd | 10 - xoi-0.68-3/xoi/man/est.coi.um.Rd | 6 xoi-0.68-3/xoi/man/est.recrate.Rd | 4 xoi-0.68-3/xoi/man/find.breaks.Rd | 12 - xoi-0.68-3/xoi/man/first.given.two.Rd | 16 +- xoi-0.68-3/xoi/man/firstden.Rd | 14 - xoi-0.68-3/xoi/man/fitGamma.Rd | 21 +- xoi-0.68-3/xoi/man/fitStahl.Rd | 22 +-- xoi-0.68-3/xoi/man/gammacoi.Rd | 16 +- xoi-0.68-3/xoi/man/intensity.Rd | 4 xoi-0.68-3/xoi/man/ioden.Rd | 14 - xoi-0.68-3/xoi/man/joint.given.two.Rd | 16 +- xoi-0.68-3/xoi/man/kfunc.Rd | 2 xoi-0.68-3/xoi/man/location.given.one.Rd | 14 - xoi-0.68-3/xoi/man/recrate2scanone.Rd | 12 - xoi-0.68-3/xoi/man/simStahl.Rd | 8 - xoi-0.68-3/xoi/man/stahlLoglik.Rd | 8 - xoi-0.68-3/xoi/man/stahlcoi.Rd | 12 - xoi-0.68-3/xoi/man/xoiversion.Rd | 2 xoi-0.68-3/xoi/man/xoprob.Rd | 14 - 46 files changed, 440 insertions(+), 428 deletions(-)
Title: Structural Data for Norway
Description: Provides structural data for Norway. Datasets relating to maps, population in municipalities, municipality/county matching, and how different municipalities have merged/redistricted over time from 2006 to 2019.
Author: Richard White [aut, cre]
Maintainer: Richard White <w@rwhite.no>
Diff between fhidata versions 2019.4.2 dated 2019-04-04 and 2019.5.19 dated 2019-05-21
DESCRIPTION | 10 MD5 | 32 +-- NEWS.md | 4 R/data_gen_all.r | 4 R/data_norway_map.R | 26 ++ R/onAttach.R | 2 data/countries_nb_to_en.rda |binary data/norway_locations_current.rda |binary data/norway_locations_long_current.rda |binary data/norway_locations_long_original.rda |binary data/norway_locations_original.rda |binary data/norway_map_counties.rda |binary data/norway_map_municips.rda |binary data/norway_municip_merging.rda |binary data/norway_population_current.rda |binary data/norway_population_original.rda |binary inst/doc/datasets.html | 328 ++++++++++++++++++++++++++------ 17 files changed, 320 insertions(+), 86 deletions(-)
Title: Identify Sudden Gains in Longitudinal Data
Description: Identify sudden gains based on the three criteria outlined by Tang and DeRubeis (1999) <doi:10.1037/0022-006X.67.6.894> to a selection of repeated measures. Sudden losses, defined as the opposite of sudden gains can also be identified. Two different datasets can be created, one including all sudden gains/losses and one including one selected sudden gain/loss for each case. It can extract scores around sudden gains/losses. It can plot the average change around sudden gains/losses and trajectories of individual cases.
Author: Milan Wiedemann [aut, cre] (<https://orcid.org/0000-0003-1991-282X>),
Graham M Thew [ctb] (<https://orcid.org/0000-0003-2851-1315>),
Richard Stott [ctb] (<https://orcid.org/0000-0003-2533-5504>),
Anke Ehlers [ctb, ths] (<https://orcid.org/0000-0002-8742-0192>)
Maintainer: Milan Wiedemann <milan.wiedemann@gmail.com>
Diff between suddengains versions 0.2.0 dated 2019-05-11 and 0.2.1 dated 2019-05-21
DESCRIPTION | 14 +-- MD5 | 48 +++++----- NEWS.md | 6 + R/create_byperson.R | 5 - R/create_bysg.R | 5 - R/identify_sg.R | 34 +++---- R/identify_sl.R | 32 +++---- R/write_byperson.R | 5 - R/write_bysg.R | 5 - README.md | 6 - build/vignette.rds |binary data/sgdata.RData |binary data/sgdata_bad.RData |binary inst/CITATION | 2 inst/doc/suddengains-tutorial.R | 41 +++++--- inst/doc/suddengains-tutorial.Rmd | 51 +++++++---- inst/doc/suddengains-tutorial.html | 169 +++++++++++++++++++------------------ man/create_byperson.Rd | 6 + man/create_bysg.Rd | 7 + man/identify_sg.Rd | 7 + man/identify_sl.Rd | 7 + man/write_byperson.Rd | 12 +- man/write_bysg.Rd | 10 +- vignettes/r-references.bib | 2 vignettes/suddengains-tutorial.Rmd | 51 +++++++---- 25 files changed, 304 insertions(+), 221 deletions(-)
Title: Single Cell Genomics for Enhancing Cell Composition Inference
from Bulk Genomics Data
Description: Cellular population mapping (CPM) a deconvolution algorithm in which single-cell genomics is required in only one or a few samples, where in other samples of the same tissue, only bulk genomics is measured and the underlying fine resolution cellular heterogeneity is inferred.
Author: Amit Frishberg [aut, cre], Naama Peshes-Yaloz [aut], Irit Gat-Viks [aut]
Maintainer: Amit Frishberg <amfrishberg@gmail.com>
Diff between scBio versions 0.1.4 dated 2019-03-29 and 0.1.5 dated 2019-05-21
DESCRIPTION | 10 ++++++---- MD5 | 6 +++--- R/scBio.R | 29 +++++++++++++++++++++++------ man/CPM.Rd | 11 +++++++---- 4 files changed, 39 insertions(+), 17 deletions(-)
Title: Simple Fisheries Stock Assessment Methods
Description: A variety of simple fish stock assessment methods.
Detailed vignettes are available on the fishR website <http://derekogle.com/fishR/>.
Author: Derek Ogle [aut, cre] (<https://orcid.org/0000-0002-0370-9299>),
Powell Wheeler [aut] (Added method='Burnham' to removal()),
Alexis Dinno [aut] (Provided base functionality of dunnTest())
Maintainer: Derek Ogle <derek@derekogle.com>
Diff between FSA versions 0.8.23 dated 2019-05-02 and 0.8.24 dated 2019-05-21
DESCRIPTION | 8 ++--- MD5 | 68 +++++++++++++++++++++++++------------------------- NEWS.md | 3 ++ R/BluegillJL.R | 9 +++++- R/BrookTroutTH.R | 5 ++- R/ChinookArg.R | 4 +- R/CodNorwegian.R | 5 ++- R/CutthroatAL.R | 9 +++++- R/Ecoli.R | 5 ++- R/Mirex.R | 5 ++- R/PSDlit.R | 3 +- R/PikeNY.R | 6 +++- R/PikeNYPartial1.R | 7 ++++- R/SMBassLS.R | 7 ++++- R/SMBassWB.R | 5 ++- R/SpotVA1.R | 3 +- R/WR79.R | 2 - R/WSlit.R | 8 +++-- R/WhitefishLC.R | 5 ++- man/BluegillJL.Rd | 9 +++++- man/BrookTroutTH.Rd | 5 ++- man/ChinookArg.Rd | 4 +- man/CodNorwegian.Rd | 5 ++- man/CutthroatAL.Rd | 9 +++++- man/Ecoli.Rd | 5 ++- man/Mirex.Rd | 5 ++- man/PSDlit.Rd | 3 +- man/PikeNY.Rd | 6 +++- man/PikeNYPartial1.Rd | 7 ++++- man/SMBassLS.Rd | 7 ++++- man/SMBassWB.Rd | 5 ++- man/SpotVA1.Rd | 3 +- man/WR79.Rd | 2 - man/WSlit.Rd | 8 +++-- man/WhitefishLC.Rd | 5 ++- 35 files changed, 167 insertions(+), 88 deletions(-)
Title: Flexible Procedures for Clustering
Description: Various methods for clustering and cluster validation.
Fixed point clustering. Linear regression clustering. Clustering by
merging Gaussian mixture components. Symmetric
and asymmetric discriminant projections for visualisation of the
separation of groupings. Cluster validation statistics
for distance based clustering including corrected Rand index.
Standardisation of cluster validation statistics by random clusterings and
comparison between many clustering methods and numbers of clusters based on
this.
Cluster-wise cluster stability assessment. Methods for estimation of
the number of clusters: Calinski-Harabasz, Tibshirani and Walther's
prediction strength, Fang and Wang's bootstrap stability.
Gaussian/multinomial mixture fitting for mixed
continuous/categorical variables. Variable-wise statistics for cluster
interpretation. DBSCAN clustering. Interface functions for many
clustering methods implemented in R, including estimating the number of
clusters with kmeans, pam and clara. Modality diagnosis for Gaussian
mixtures. For an overview see package?fpc.
Author: Christian Hennig <christian.hennig@unibo.it>
Maintainer: Christian Hennig <christian.hennig@unibo.it>
Diff between fpc versions 2.1-11.2 dated 2019-04-22 and 2.2-1 dated 2019-05-21
DESCRIPTION | 28 MD5 | 180 ++--- NAMESPACE | 14 R/clusterboot.R | 142 ++-- R/cquality18.R |only R/fixreg.R | 3 man/adcoord.Rd | 4 man/ancoord.Rd | 4 man/awcoord.Rd | 4 man/batcoord.Rd | 4 man/bhattacharyya.dist.Rd | 4 man/bhattacharyya.matrix.Rd | 6 man/calinhara.Rd | 4 man/can.Rd | 4 man/cat2bin.Rd | 6 man/cdbw.Rd | 4 man/cgrestandard.Rd |only man/classifdist.Rd | 6 man/clucols.Rd | 4 man/clujaccard.Rd | 4 man/clusexpect.Rd | 4 man/clustatsum.Rd |only man/cluster.magazine.Rd |only man/cluster.stats.Rd | 14 man/cluster.varstats.Rd | 4 man/clusterbenchstats.Rd |only man/clusterboot.Rd | 7 man/cmahal.Rd | 4 man/concomp.Rd | 4 man/confusion.Rd | 4 man/cov.wml.Rd | 4 man/cqcluster.stats.Rd |only man/cvnn.Rd | 4 man/cweight.Rd | 4 man/dipp.tantrum.Rd | 4 man/diptest.multi.Rd | 4 man/discrcoord.Rd | 4 man/discrete.recode.Rd | 4 man/discrproj.Rd | 4 man/distancefactor.Rd | 4 man/distcritmulti.Rd | 4 man/distrsimilarity.Rd |only man/dridgeline.Rd | 4 man/dudahart2.Rd | 4 man/extract.mixturepars.Rd | 4 man/findrep.Rd | 4 man/fixmahal.Rd | 6 man/fixreg.Rd | 4 man/flexmixedruns.Rd | 4 man/fpc-package.Rd | 28 man/fpclusters.Rd | 4 man/itnumber.Rd | 4 man/jittervar.Rd | 4 man/kmeansCBI.Rd | 38 - man/kmeansruns.Rd | 4 man/lcmixed.Rd | 4 man/localshape.Rd | 4 man/mahalanodisc.Rd | 4 man/mahalanofix.Rd | 4 man/mahalconf.Rd | 4 man/mergenormals.Rd | 4 man/mergeparameters.Rd | 4 man/minsize.Rd | 4 man/mixdens.Rd | 4 man/mixpredictive.Rd | 4 man/mvdcoord.Rd | 4 man/ncoord.Rd | 4 man/neginc.Rd | 4 man/nselectboot.Rd | 12 man/pamk.Rd | 4 man/piridge.Rd | 4 man/piridge.zeroes.Rd | 4 man/plot.valstat.Rd |only man/plotcluster.Rd | 4 man/prediction.strength.Rd | 16 man/rFace.Rd | 4 man/randcmatrix.Rd | 4 man/randconf.Rd | 4 man/randomclustersim.Rd |only man/regmix.Rd | 4 man/ridgeline.Rd | 4 man/ridgeline.diagnosis.Rd | 4 man/simmatrix.Rd | 4 man/solvecov.Rd | 4 man/sseg.Rd | 4 man/stupidkcentroids.Rd |only man/stupidknn.Rd |only man/tdecomp.Rd | 4 man/unimodal.ind.Rd | 4 man/valstat.object.Rd |only man/weightplots.Rd | 4 man/wfu.Rd | 4 man/xtable.Rd | 4 man/zmisclassification.matrix.Rd | 4 tests/Examples/fpc-Ex.Rout.save | 1361 ++++++++++++++++++++++++++++++++++++++- tests/fpctests_notallin.R | 18 tests/fpctests_notallin.Rout | 212 +++++- 97 files changed, 1999 insertions(+), 366 deletions(-)
Title: Automatic Codebooks from Metadata Encoded in Dataset Attributes
Description: Easily automate the following tasks to describe data frames:
Summarise the distributions, and labelled missings of variables graphically
and using descriptive statistics.
For surveys, compute and summarise reliabilities (internal consistencies,
retest, multilevel) for psychological scales.
Combine this information with metadata (such as item labels and labelled
values) that is derived from R attributes.
To do so, the package relies on 'rmarkdown' partials, so you can generate
HTML, PDF, and Word documents.
Codebooks are also available as tables (CSV, Excel, etc.) and in JSON-LD, so
that search engines can find your data and index the metadata.
The metadata are also available at your fingertips via RStudio Addins.
Author: Ruben Arslan [aut, cre]
Maintainer: Ruben Arslan <ruben.arslan@gmail.com>
Diff between codebook versions 0.8.0 dated 2019-02-21 and 0.8.1 dated 2019-05-21
DESCRIPTION | 6 LICENSE | 2 MD5 | 36 NEWS.md | 7 R/codebook.R | 8 R/create_metadata.R | 4 R/misc.R | 12 R/reliability.R | 5 README.md | 42 inst/_codebook_scale.Rmd | 2 inst/doc/codebook.R | 4 inst/doc/codebook.html | 26 inst/doc/codebook_qualtrics.html | 205 +-- inst/doc/codebook_sav.html | 19 inst/doc/codebook_tutorial.R | 2100 ++++++++++++++++++++++++++++++++------- inst/doc/codebook_tutorial.Rmd | 149 +- inst/doc/codebook_tutorial.html | 1976 +++++++++++++++++------------------- man/md_pattern.Rd | 2 vignettes/codebook_tutorial.Rmd | 149 +- 19 files changed, 2991 insertions(+), 1763 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-10-08 0.18
2018-03-16 0.17
2018-03-16 0.17-1
2017-11-24 0.16-6
2017-11-16 0.16-5
Title: Inhomogeneous Poisson Point Processes
Description: Generates random numbers corresponding to the events on a Poisson point process with changing event rates. This includes the possibility to incorporate additional information such as the number of events occurring or the location of an already known event. It can also generate the probability density functions of specific events in the cases where additional information is available. Based on Hohmann (2019) <arXiv:1901.10754>.
Author: Niklas Hohmann
Maintainer: Niklas Hohmann <Niklas.Hohmann@fau.de>
Diff between IPPP versions 1.0 dated 2019-02-06 and 1.1 dated 2019-05-21
IPPP-1.0/IPPP/inst/doc/Introduction_to_the_package_IPPP.R |only IPPP-1.0/IPPP/inst/doc/Introduction_to_the_package_IPPP.Rmd |only IPPP-1.0/IPPP/inst/doc/Introduction_to_the_package_IPPP.html |only IPPP-1.0/IPPP/vignettes/Introduction_to_the_package_IPPP.Rmd |only IPPP-1.1/IPPP/DESCRIPTION | 8 +-- IPPP-1.1/IPPP/MD5 | 28 +++++------ IPPP-1.1/IPPP/build/partial.rdb |binary IPPP-1.1/IPPP/build/vignette.rds |binary IPPP-1.1/IPPP/inst/doc/IPPP.R |only IPPP-1.1/IPPP/inst/doc/IPPP.Rmd |only IPPP-1.1/IPPP/inst/doc/IPPP.html |only IPPP-1.1/IPPP/man/IPPP-package.Rd | 10 +++ IPPP-1.1/IPPP/man/IPPPcond.Rd | 10 +++ IPPP-1.1/IPPP/man/IPPPconddens.Rd | 13 ++++- IPPP-1.1/IPPP/man/IPPPcondrandnum.Rd | 9 +++ IPPP-1.1/IPPP/man/IPPPinterval.Rd | 9 +++ IPPP-1.1/IPPP/man/IPPPnthpointdens.Rd | 12 +++- IPPP-1.1/IPPP/man/IPPPuncond.Rd | 12 +++- IPPP-1.1/IPPP/vignettes/IPPP.Rmd |only 19 files changed, 81 insertions(+), 30 deletions(-)
Title: Doubly Robust Generalized Estimating Equations
Description: Fit restricted mean models for the conditional association
between an exposure and an outcome, given covariates. Three methods
are implemented: O-estimation, where a nuisance model for the
association between the covariates and the outcome is used;
E-estimation where a nuisance model for the association
between the covariates and the exposure is used, and doubly robust (DR)
estimation where both nuisance models are used. In DR-estimation,
the estimates will be consistent when at least one of the nuisance
models is correctly specified, not necessarily both. For more information, see Zetterqvist and Sjölander (2015) <doi:10.1515/em-2014-0021>.
Author: Johan Zetterqvist <drjohanzetterqvist at gmail.com> , Arvid Sjölander <arvid.sjolander at ki.se> with contributions from Alexander Ploner.
Maintainer: Johan Zetterqvist <drjohanzetterqvist@gmail.com>
Diff between drgee versions 1.1.6 dated 2016-11-08 and 1.1.8 dated 2019-05-21
drgee-1.1.6/drgee/R/findRoots.R |only drgee-1.1.6/drgee/R/robVcov.R |only drgee-1.1.6/drgee/src/center.cpp |only drgee-1.1.6/drgee/src/condit.cpp |only drgee-1.1.8/drgee/DESCRIPTION | 14 drgee-1.1.8/drgee/MD5 | 50 +- drgee-1.1.8/drgee/NAMESPACE | 15 drgee-1.1.8/drgee/NEWS | 37 + drgee-1.1.8/drgee/R/conditFit.R | 81 +-- drgee-1.1.8/drgee/R/drConditFit.R | 473 ++++++++++++++----- drgee-1.1.8/drgee/R/drFit.R | 9 drgee-1.1.8/drgee/R/dreFit.R | 34 - drgee-1.1.8/drgee/R/dreFitCond.R | 27 - drgee-1.1.8/drgee/R/drgee.R | 60 ++ drgee-1.1.8/drgee/R/drgeeData.R | 468 +++++++++++++++--- drgee-1.1.8/drgee/R/gee.R | 115 ++++ drgee-1.1.8/drgee/R/geeFit.R | 47 - drgee-1.1.8/drgee/R/geeFitCond.R | 9 drgee-1.1.8/drgee/R/helpFunctions.R |only drgee-1.1.8/drgee/R/oFit.R | 22 drgee-1.1.8/drgee/R/vcov.R |only drgee-1.1.8/drgee/man/centerX.Rd |only drgee-1.1.8/drgee/man/drgee.Rd | 43 + drgee-1.1.8/drgee/man/drgeeData.Rd | 21 drgee-1.1.8/drgee/man/gee.Rd | 20 drgee-1.1.8/drgee/man/getScoreResidualsFromClogit.Rd | 6 drgee-1.1.8/drgee/man/robVcov.Rd | 22 drgee-1.1.8/drgee/src/Makevars | 5 drgee-1.1.8/drgee/src/Makevars.win | 5 drgee-1.1.8/drgee/src/drgee.cpp |only 30 files changed, 1194 insertions(+), 389 deletions(-)
Title: Enumeration and Uniform Sampling of Transmission Trees for a
Known Phylogeny
Description: For a single, known pathogen phylogeny, provides functions for enumeration of the set of compatible epidemic transmission trees, and for uniform sampling from that set. Optional arguments allow for incomplete sampling with a known number of missing individuals, multiple sampling, and known infection time limits. Always assumed are a complete transmission bottleneck and no superinfection or reinfection. See Hall and Colijn (2019) <doi:10.1093/molbev/msz058> for methodology.
Author: Matthew Hall [aut, cre],
Caroline Colijn [ctb]
Maintainer: Matthew Hall <matthew.hall@bdi.ox.ac.uk>
Diff between STraTUS versions 1.1 dated 2019-03-18 and 1.1.1 dated 2019-05-21
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- R/sampling.R | 20 +++++++------------- 3 files changed, 15 insertions(+), 21 deletions(-)
Title: R6 Reference Class Based Data Structures
Description: Provides reference classes implementing some useful data structures.
The package implements these data structures by using the reference class R6.
Therefore, the classes of the data structures are also reference classes which means that their instances are passed by reference.
The implemented data structures include stack, queue, double-ended queue, doubly linked list, set, dictionary and binary search tree.
See for example <https://en.wikipedia.org/wiki/Data_structure> for more information about the data structures.
Author: Yukai Yang [aut, cre] (<https://orcid.org/0000-0002-2623-8549>)
Maintainer: Yukai Yang <yukai.yang@statistik.uu.se>
Diff between R6DS versions 1.1.0 dated 2019-05-14 and 1.2.0 dated 2019-05-21
DESCRIPTION | 8 - MD5 | 45 ++++---- NEWS.md | 20 +++ R/R6DS.R | 22 +++ R/RBST.R | 106 +++++++++++++------ R/RDLL.R | 323 +++++++++------------------------------------------------- R/RDeque.R | 216 +++++++++++++++----------------------- R/RDict.R | 160 ++++++++++------------------ R/RQueue.R | 112 +++++++++++--------- R/RSet.R | 105 +++++++++--------- R/RStack.R | 77 +++++++++---- R/utils.R | 2 README.md | 94 +++++++++++++++- build |only inst |only man/R6DS.Rd | 22 +++ man/RBST.Rd | 57 ++++++---- man/RDLL.Rd | 78 +++++--------- man/RDeque.Rd | 57 ++++------ man/RDict.Rd | 55 +++------ man/RQueue.Rd | 38 ++++-- man/RSet.Rd | 52 +++++---- man/RStack.Rd | 38 ++++-- vignettes |only 24 files changed, 803 insertions(+), 884 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package 'pan', 'jomo' is a package for multilevel joint modelling multiple imputation (Carpenter and Kenward, 2013) <doi: 10.1002/9781119942283>.
Novel aspects of 'jomo' are the possibility of handling binary and categorical data through latent normal variables, the option to use cluster-specific covariance matrices and to impute compatibly with the substantive model.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <m.quartagno@ucl.ac.uk>
Diff between jomo versions 2.6-7 dated 2019-02-06 and 2.6-8 dated 2019-05-21
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/jomo.lmer.MCMCchain.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Adaptive Sampling for Positive Unlabeled and Label Noise
Learning
Description: Implements the adaptive sampling procedure, a framework for both positive unlabeled learning and learning with class label noise. Yang, P., Ormerod, J., Liu, W., Ma, C., Zomaya, A., Yang, J. (2018) <doi:10.1109/TCYB.2018.2816984>.
Author: Pengyi Yang
Maintainer: Pengyi Yang <yangpy7@gmail.com>
Diff between AdaSampling versions 1.1 dated 2018-06-27 and 1.3 dated 2019-05-21
DESCRIPTION | 10 ++--- MD5 | 20 +++++----- NAMESPACE | 4 +- R/adaSample.R | 18 +++++---- R/adaSvmBenchmark.R | 1 R/singleIter.R | 31 +++++++++++++--- R/weightedKNN.R |only build/vignette.rds |binary inst/doc/vignette.html | 93 +++++++++++++++++++++++++++++++------------------ man/adaSample.Rd | 14 ++++--- man/singleIter.Rd | 14 ++++--- man/weightedKNN.Rd |only 12 files changed, 131 insertions(+), 74 deletions(-)
Title: Miscellaneous Functions from M. Kohl
Description: Contains several functions for statistical data analysis; e.g. for sample size and power calculations, computation of confidence intervals and tests, and generation of similarity matrices.
Author: Matthias Kohl [aut, cre] (<https://orcid.org/0000-0001-9514-8910>)
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between MKmisc versions 1.3 dated 2019-04-14 and 1.4 dated 2019-05-21
DESCRIPTION | 8 - MD5 | 18 +- NEWS | 8 + R/perfMeasures.R | 55 ++++--- inst/doc/MKmisc.R | 2 inst/doc/MKmisc.Rmd | 6 inst/doc/MKmisc.html | 400 ++++++++++++++++++++++++++------------------------- man/binomCI.Rd | 2 man/perfMeasures.Rd | 27 ++- vignettes/MKmisc.Rmd | 6 10 files changed, 291 insertions(+), 241 deletions(-)
Title: Areal Weighted Interpolation
Description: A pipeable, transparent implementation of areal weighted interpolation
with support for interpolating multiple variables in a single function call.
These tools provide a full-featured workflow for validation and estimation
that fits into both modern data management (e.g. tidyverse) and spatial
data (e.g. sf) frameworks.
Author: Christopher Prener [aut, cre] (<https://orcid.org/0000-0002-4310-9888>),
Charlie Revord [aut]
Maintainer: Christopher Prener <chris.prener@slu.edu>
Diff between areal versions 0.1.2 dated 2018-12-31 and 0.1.5 dated 2019-05-21
areal-0.1.2/areal/man/ar_validate_crs.Rd |only areal-0.1.2/areal/man/ar_validate_longlat.Rd |only areal-0.1.2/areal/man/ar_validate_sf.Rd |only areal-0.1.2/areal/man/ar_validate_vars_conflict.Rd |only areal-0.1.2/areal/man/ar_validate_vars_exist.Rd |only areal-0.1.2/areal/man/aw_area.Rd |only areal-0.1.2/areal/man/aw_calculate_weight.Rd |only areal-0.1.2/areal/man/aw_interpolate_multiple.Rd |only areal-0.1.2/areal/man/aw_interpolate_single.Rd |only areal-0.1.2/areal/man/aw_interpolater.Rd |only areal-0.1.2/areal/man/aw_strip_df.Rd |only areal-0.1.2/areal/man/aw_validate_preview.Rd |only areal-0.1.5/areal/DESCRIPTION | 8 areal-0.1.5/areal/MD5 | 58 - areal-0.1.5/areal/NAMESPACE | 7 areal-0.1.5/areal/NEWS.md | 47 areal-0.1.5/areal/R/ar_validate.R | 133 +- areal-0.1.5/areal/R/aw_interpolate.R | 236 ++-- areal-0.1.5/areal/R/aw_intersect.R | 49 areal-0.1.5/areal/R/aw_preview_weights.R | 30 areal-0.1.5/areal/README.md | 23 areal-0.1.5/areal/build/vignette.rds |binary areal-0.1.5/areal/inst/CITATION |only areal-0.1.5/areal/inst/doc/areal-weighted-interpolation.R | 33 areal-0.1.5/areal/inst/doc/areal-weighted-interpolation.Rmd | 40 areal-0.1.5/areal/inst/doc/areal-weighted-interpolation.html | 542 ++++++----- areal-0.1.5/areal/inst/doc/areal.html | 9 areal-0.1.5/areal/inst/doc/data-preparation.Rmd | 2 areal-0.1.5/areal/inst/doc/data-preparation.html | 11 areal-0.1.5/areal/inst/testdata/geometryCollection.rda |only areal-0.1.5/areal/man/figures/arealLogo.png |binary areal-0.1.5/areal/tests/testthat/test_aw_interpolate.R | 25 areal-0.1.5/areal/tests/testthat/test_aw_intersect.R | 9 areal-0.1.5/areal/tests/testthat/test_aw_preview_weights.R | 8 areal-0.1.5/areal/tests/testthat/test_aw_verify.R | 2 areal-0.1.5/areal/vignettes/areal-weighted-interpolation.Rmd | 40 areal-0.1.5/areal/vignettes/data-preparation.Rmd | 2 37 files changed, 794 insertions(+), 520 deletions(-)
Title: Toolkit to Validate New Data for a Predictive Model
Description: A lightweight toolkit to validate new observations when computing
their predictions with a predictive model. The validation process
consists of two steps: (1) record relevant statistics and meta data of the
variables in the original training data for the predictive model and
(2) use these data to run a set of basic validation tests on the new set of
observations.
Author: Lars Kjeldgaard [aut, cre]
Maintainer: Lars Kjeldgaard <lars_kjeldgaard@hotmail.com>
Diff between recorder versions 0.8.0 dated 2019-05-20 and 0.8.1 dated 2019-05-21
recorder-0.8.0/recorder/README.md |only recorder-0.8.0/recorder/man/figures |only recorder-0.8.1/recorder/DESCRIPTION | 6 +++--- recorder-0.8.1/recorder/MD5 | 12 +++++++----- recorder-0.8.1/recorder/build |only recorder-0.8.1/recorder/inst/doc |only recorder-0.8.1/recorder/inst/extdata/config.yml | 2 +- recorder-0.8.1/recorder/vignettes |only 8 files changed, 11 insertions(+), 9 deletions(-)
Title: Drawing Survival Curves using 'ggplot2'
Description: Contains the function 'ggsurvplot()' for drawing easily beautiful
and 'ready-to-publish' survival curves with the 'number at risk' table
and 'censoring count plot'. Other functions are also available to plot
adjusted curves for `Cox` model and to visually examine 'Cox' model assumptions.
Author: Alboukadel Kassambara [aut, cre],
Marcin Kosinski [aut],
Przemyslaw Biecek [ctb],
Scheipl Fabian [ctb]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between survminer versions 0.4.3 dated 2018-08-04 and 0.4.4 dated 2019-05-21
DESCRIPTION | 11 - MD5 | 76 ++++---- NEWS.md | 19 ++ R/ggadjustedcurves.R | 26 +- R/ggforest.R | 31 ++- R/ggsurvplot_core.R | 7 R/ggsurvplot_df.R | 30 --- R/surv_summary.R | 6 R/utilities.R | 3 README.md | 5 inst/doc/Informative_Survival_Plots.html | 72 +++++++ inst/doc/Playing_with_fonts_and_texts.html | 80 +++++++- inst/doc/Specifiying_weights_in_log-rank_comparisons.Rmd | 12 - inst/doc/Specifiying_weights_in_log-rank_comparisons.html | 94 ++++++++-- man/arrange_ggsurvplots.Rd | 4 man/ggadjustedcurves.Rd | 18 - man/ggcompetingrisks.Rd | 5 man/ggcoxfunctional.Rd | 4 man/ggcoxzph.Rd | 4 man/ggflexsurvplot.Rd | 3 man/ggforest.Rd | 5 man/ggsurvevents.Rd | 6 man/ggsurvplot.Rd | 15 - man/ggsurvplot_add_all.Rd | 4 man/ggsurvplot_combine.Rd | 9 man/ggsurvplot_df.Rd | 11 - man/ggsurvplot_facet.Rd | 10 - man/ggsurvtable.Rd | 8 man/ggsurvtheme.Rd | 10 - man/pairwise_survdiff.Rd | 3 man/surv_cutpoint.Rd | 4 man/surv_pvalue.Rd | 4 tools/README-ggplot2-basic-survival-plot-1.png |binary tools/README-ggplot2-customized-survival-plot-1.png |binary tools/README-ggplot2-more-customized-survival-plot-1.png |binary tools/README-ggplot2-uber-customized-survival-plot-1.png |binary tools/README-ggplot2-uber-platinium-customized-survival-plot-1.png |binary tools/README-ggplot2-uber-platinium-premium-customized-survival-plot-1.png |binary vignettes/Specifiying_weights_in_log-rank_comparisons.Rmd | 12 - 39 files changed, 416 insertions(+), 195 deletions(-)
Title: (Permuted) Brunner-Munzel Test
Description: Provides the functions for Brunner-Munzel test and
permuted Brunner-Munzel test,
which enable to use formula, matrix, and table as argument.
These functions are based on Brunner and Munzel (2000)
<doi:10.1002/(SICI)1521-4036(200001)42:1%3C17::AID-BIMJ17%3E3.0.CO;2-U>
and Neubert and Brunner (2007) <doi:10.1016/j.csda.2006.05.024>,
and are written with FORTRAN.
Author: Toshiaki Ara [aut, cre]
Maintainer: Toshiaki Ara <toshiaki.ara@gmail.com>
Diff between brunnermunzel versions 1.3.3 dated 2019-04-10 and 1.3.4 dated 2019-05-21
DESCRIPTION | 10 - MD5 | 11 + NEWS.md | 3 build/vignette.rds |binary inst/doc/usage.html | 305 ++++++++++++++++++++++++++-------------------------- src/Makevars |only src/bm_test.f | 2 7 files changed, 170 insertions(+), 161 deletions(-)