Title: An S4 Lattice-Based Package for the Representation of
Multivariate Data
Description: Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.
Author: Stéphane Dray <stephane.dray@univ-lyon1.fr> and Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>, with contributions from Jean Thioulouse. Based on earlier work by Alice Julien-Laferrière.
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between adegraphics versions 1.0-7 dated 2017-03-23 and 1.0-8 dated 2017-04-11
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/ade4-plot.R | 3 ++- inst/doc/adegraphics.html | 16 ++++++++-------- man/adegraphics-package.Rd | 4 ++-- man/s.logo.Rd | 9 ++++----- 6 files changed, 25 insertions(+), 25 deletions(-)
Title: Client for the YouTube API
Description: Get comments posted on YouTube videos, information on how many
times a video has been liked, search for videos with particular content, and
much more. You can also scrape captions from a few videos. To learn more about
the YouTube API, see <https://developers.google.com/youtube/v3/>.
Author: Gaurav Sood [aut, cre]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between tuber versions 0.7.0 dated 2016-11-21 and 0.8.0 dated 2017-04-11
DESCRIPTION | 8 +-- MD5 | 86 +++++++++++++++++++-------------------- NEWS.md | 4 + R/get_captions.R | 2 R/get_channel_stats.R | 2 R/get_comments.R | 2 R/get_playlists.R | 4 + R/get_stats.R | 2 R/get_video_details.R | 2 R/list_caption_tracks.R | 2 R/list_channel_activities.R | 2 R/yt_search.R | 80 ++++++++++++++++++++++++++++-------- README.md | 1 build/vignette.rds |binary inst/doc/tuber-ex.html | 6 +- man/get_captions.Rd | 1 man/get_channel_stats.Rd | 1 man/get_comment_threads.Rd | 1 man/get_comments.Rd | 1 man/get_playlist_items.Rd | 1 man/get_playlists.Rd | 4 - man/get_related_videos.Rd | 1 man/get_stats.Rd | 1 man/get_subscriptions.Rd | 1 man/get_video_details.Rd | 1 man/list_abuse_report_reasons.Rd | 1 man/list_caption_tracks.Rd | 1 man/list_channel_activities.Rd | 1 man/list_channel_resources.Rd | 1 man/list_channel_sections.Rd | 1 man/list_channel_videos.Rd | 1 man/list_guidecats.Rd | 1 man/list_langs.Rd | 1 man/list_regions.Rd | 1 man/list_videocats.Rd | 1 man/list_videos.Rd | 1 man/tuber.Rd | 1 man/tuber_GET.Rd | 1 man/tuber_POST.Rd | 1 man/tuber_check.Rd | 1 man/yt_check_token.Rd | 1 man/yt_oauth.Rd | 1 man/yt_search.Rd | 28 ++++++------ man/yt_topic_search.Rd | 1 44 files changed, 143 insertions(+), 119 deletions(-)
Title: Phylogenetic ANalyses of DiversificAtion
Description: Implements macroevolutionary analyses on phylogenetic trees. See
Morlon et al. (2010) <DOI:10.1371/journal.pbio.1000493>, Morlon et al. (2011)
<DOI:10.1073/pnas.1102543108>, Condamine et al. (2013) <DOI:10.1111/ele.12062>,
Morlon et al. (2014) <DOI:10.1111/ele.12251>, Manceau et al. (2015) <DOI:
10.1111/ele.12415>, Lewitus & Morlon (2016) <DOI:10.1093/sysbio/syv116>, Drury
et al. (2016) <DOI:10.1093/sysbio/syw020>, Manceau et al. (2016) <DOI:10.1093/sysbio/syw115>,
and Clavel & Morlon (2017) <DOI:10.1073/pnas.1606868114>.
Author: Hélène Morlon [aut, cre, cph],
Eric Lewitus [aut, cph],
Fabien Condamine [aut, cph],
Marc Manceau [aut, cph],
Julien Clavel [aut, cph],
Jonathan Drury [aut, cph]
Maintainer: Hélène Morlon <morlon@biologie.ens.fr>
Diff between RPANDA versions 1.2 dated 2016-03-31 and 1.3 dated 2017-04-11
DESCRIPTION | 38 +++- MD5 | 87 ++++++++-- NAMESPACE | 21 +- R/CreateBioGeoB_Object_subclade.R |only R/CreateGeoObject.R | 2 R/CreateGeoObject_BioGeoBEARS.R |only R/DDexp_geo_ADiag.R |only R/DDexp_nogeo_ADiag.R |only R/DDlin_geo_ADiag.R |only R/DDlin_nogeo_ADiag.R |only R/MC.rescale.R | 2 R/MC.rescale_geog.R | 2 R/MC_geo_PM.R |only R/MC_nogeo_ADiag.R |only R/PhenotypicModel.class.R |only R/createModel.R |only R/event_txt_into_events_row.R |only R/events_txt_into_events_table.R |only R/events_txt_list_into_events_table.R |only R/fitTipData.R |only R/fit_t_comp.R | 105 +++++------- R/fit_t_env.R |only R/getDataLikelihood.R |only R/getTipDistribution.R |only R/likelihood_t_env.R |only R/modelSelection.R |only R/plot.fit_t.env.r |only R/print.fit_t.env.R |only R/resortGeoObject.R |only R/sim.convergence.geo.R |only R/sim.divergence.geo.R |only R/sim_t_env.R |only R/simulateTipData.R |only R/spectR.R | 276 +++++++++++----------------------- R/stratified_BGB_to_tables.R |only README.md | 17 +- data/BGB.examples.rda |only inst/CITATION | 18 +- man/BGB.examples.Rd |only man/CreateGeoObject.Rd | 2 man/CreateGeoObject_BioGeoBEARS.Rd |only man/PhenotypicACDC-class.Rd |only man/PhenotypicADiag-class.Rd |only man/PhenotypicBM-class.Rd |only man/PhenotypicDD-class.Rd |only man/PhenotypicGMM-class.Rd |only man/PhenotypicModel-class.Rd |only man/PhenotypicOU-class.Rd |only man/PhenotypicPM-class.Rd |only man/RPANDA-package.Rd | 18 +- man/createModel.Rd |only man/createModelCoevolution.Rd |only man/fitTipData-methods.Rd |only man/fitTipData.Rd |only man/fit_t_comp.Rd | 23 -- man/fit_t_env.Rd |only man/getDataLikelihood-methods.Rd |only man/getDataLikelihood.Rd |only man/getTipDistribution-methods.Rd |only man/getTipDistribution.Rd |only man/likelihood_t_DD.Rd | 8 man/likelihood_t_MC.Rd | 9 - man/likelihood_t_MC_geog.Rd | 7 man/likelihood_t_env.Rd |only man/lines.fit_t.env.Rd |only man/modelSelection-methods.Rd |only man/modelSelection.Rd |only man/plot.fit_t.env.Rd |only man/sim.convergence.geo.Rd |only man/sim.divergence.geo.Rd |only man/sim_t_env.Rd |only man/simulateTipData-methods.Rd |only man/simulateTipData.Rd |only 73 files changed, 319 insertions(+), 316 deletions(-)
Title: Robust Data-Driven Statistical Inference in
Regression-Discontinuity Designs
Description: Regression-discontinuity (RD) designs are quasi-experimental research designs popular in social, behavioral and natural sciences. The RD design is usually employed to study the (local) causal effect of a treatment, intervention or policy. This package provides tools for data-driven graphical and analytical statistical inference in RD designs: rdrobust() to construct local-polynomial point estimators and robust confidence intervals for average treatment effects at the cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect() to perform bandwidth selection for the different procedures implemented, and rdplot() to conduct exploratory data analysis (RD plots).
Author: Sebastian Calonico <scalonico@bus.miami.edu>, Matias D. Cattaneo <cattaneo@umich.edu>, Max H. Farrell <max.farrell@chicagobooth.edu>, Rocio Titiunik <titiunik@umich.edu>
Maintainer: Sebastian Calonico <scalonico@bus.miami.edu>
Diff between rdrobust versions 0.96 dated 2017-03-08 and 0.97 dated 2017-04-11
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/rdrobust.R | 2 +- man/rdbwselect.Rd | 25 ++++++++----------------- man/rdbwselect_2014.Rd | 6 +++--- man/rdplot.Rd | 18 +++++------------- man/rdrobust-package.Rd | 4 ++-- man/rdrobust.Rd | 28 +++++++++------------------- man/rdrobust_RDsenate.Rd | 4 ++-- 9 files changed, 42 insertions(+), 69 deletions(-)
Title: A Plotting Toolbox for 2D Oceanographic Data
Description: Plotting toolbox for 2D oceanographic data (satellite data, sst, chla, ocean fronts & bathymetry). Recognized classes and formats include ncdf4, Raster, '.nc' and '.gz' files.
Author: Robert K. Bauer
Maintainer: Robert K. Bauer <robert.bauer@ird.fr>
Diff between oceanmap versions 0.0.4 dated 2017-03-15 and 0.0.5 dated 2017-04-11
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- R/get.bathy.r | 4 ++-- R/get.worldmap.r | 13 +++++++++---- R/plotmap.r | 30 ++++++++++++++++++++++-------- R/sysdata.rda |binary data/cmap.rda |binary data/cmap_topo.rda |binary data/parameter_definitions.rda |binary data/region_definitions.bkp.rda |binary data/region_definitions.rda |binary inst/doc/oceanmap.pdf |binary man/plotmap.Rd | 6 +++--- 14 files changed, 56 insertions(+), 34 deletions(-)
Title: Nested Association Mapping
Description: Designed for association studies in nested association mapping (NAM) panels, also handling experimental and random panels. It includes tools for genome-wide associations of multiple populations, marker quality control, population genetics analysis, genome-wide prediction, solving mixed models and finding variance components through likelihood and Bayesian methods.
Author: Alencar Xavier, William Muir, Katy Rainey, Shizhong Xu.
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between NAM versions 1.5.0 dated 2016-10-20 and 1.5.1 dated 2017-04-11
NAM-1.5.0/NAM/inst/add/modelSelect.R |only NAM-1.5.0/NAM/src/KMUP.cpp |only NAM-1.5.0/NAM/src/KMUP2.cpp |only NAM-1.5.0/NAM/src/SAMP.cpp |only NAM-1.5.0/NAM/src/SAMP2.cpp |only NAM-1.5.0/NAM/src/calcSize.cpp |only NAM-1.5.0/NAM/src/emBA.cpp |only NAM-1.5.0/NAM/src/emBB.cpp |only NAM-1.5.0/NAM/src/emBC.cpp |only NAM-1.5.0/NAM/src/emBL.cpp |only NAM-1.5.0/NAM/src/emRR.cpp |only NAM-1.5.0/NAM/src/funI.cpp |only NAM-1.5.0/NAM/src/funX.cpp |only NAM-1.5.0/NAM/src/gs.cpp |only NAM-1.5.0/NAM/src/inputRow.cpp |only NAM-1.5.0/NAM/src/timesMatrix.cpp |only NAM-1.5.0/NAM/src/timesVec.cpp |only NAM-1.5.1/NAM/DESCRIPTION | 10 +- NAM-1.5.1/NAM/MD5 | 53 +++++---------- NAM-1.5.1/NAM/NAMESPACE | 2 NAM-1.5.1/NAM/R/RcppExports.R | 32 +++++---- NAM-1.5.1/NAM/R/gmm.R | 3 NAM-1.5.1/NAM/R/snp.R | 13 ++- NAM-1.5.1/NAM/R/wgr.R | 70 +++++++++++++++----- NAM-1.5.1/NAM/build/vignette.rds |binary NAM-1.5.1/NAM/inst/add/cvNAM.R | 28 +++++--- NAM-1.5.1/NAM/inst/doc/gwa_description.pdf |binary NAM-1.5.1/NAM/inst/doc/vignette1.Rmd | 16 +++- NAM-1.5.1/NAM/inst/doc/vignette1.html | 29 +++++--- NAM-1.5.1/NAM/inst/doc/vignette2.html | 100 ++++++++++++++--------------- NAM-1.5.1/NAM/man/Internals.Rd | 6 + NAM-1.5.1/NAM/man/NAM-package.Rd | 4 - NAM-1.5.1/NAM/man/wgr.Rd | 67 ++++++++----------- NAM-1.5.1/NAM/src/Functions.cpp |only NAM-1.5.1/NAM/src/RcppExports.cpp | 86 +++++++++++++++--------- NAM-1.5.1/NAM/src/c.c |only NAM-1.5.1/NAM/vignettes/vignette1.Rmd | 16 +++- 37 files changed, 309 insertions(+), 226 deletions(-)
Title: Visualize Species Occurrence Data
Description: Utilities for visualizing species occurrence data. Includes
functions to visualize occurrence data from 'spocc', 'rgbif',
and other packages. Mapping options included for base R plots, 'ggplot2',
'ggmap', 'leaflet' and 'GitHub' 'gists'.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between mapr versions 0.3.0 dated 2016-11-05 and 0.3.4 dated 2017-04-11
DESCRIPTION | 14 ++--- LICENSE | 2 MD5 | 56 ++++++++++----------- NAMESPACE | 4 - NEWS.md | 15 +++++ R/colors.R | 6 +- R/hull.R | 6 +- R/map_ggmap.R | 22 ++++++-- R/map_ggplot.R | 4 - R/map_gist.R | 20 +++---- R/map_leaflet.R | 2 R/map_plot.R | 9 +-- R/mapr-package.R | 41 ++++++--------- R/occ2sp.R | 4 - R/util_github.r | 24 +++++---- R/zzz.r | 3 - build/vignette.rds |binary man/gbif_eg1.Rd | 7 -- man/hull.Rd | 25 +++++++-- man/map_ggmap.Rd | 14 ++++- man/map_ggplot.Rd | 38 +++++++++++++- man/map_gist.Rd | 11 +--- man/map_leaflet.Rd | 3 - man/map_plot.Rd | 58 +++++++++++++++++++++ man/mapr-package.Rd | 36 ++++++------- man/occ2sp.Rd | 3 - man/occdat_eg1.Rd | 7 -- man/style_geojson.Rd | 5 - tests/testthat/test-map_ggmap.R | 106 ++++++++++++++++++++-------------------- 29 files changed, 340 insertions(+), 205 deletions(-)
Title: Kernel Smoothing for Bivariate Copula Densities
Description: Provides fast implementations of kernel smoothing techniques for
bivariate copula densities, in particular density estimation and resampling.
Author: Thomas Nagler [aut, cre],
Kuangyu Wen [ctb]
Maintainer: Thomas Nagler <thomas.nagler@tum.de>
Diff between kdecopula versions 0.8.0 dated 2016-12-25 and 0.8.1 dated 2017-04-11
DESCRIPTION | 8 - MD5 | 79 ++++++------- NAMESPACE | 2 NEWS.md | 12 ++ R/RcppExports.R | 182 +------------------------------ R/bandwidths.R | 178 +++++++++++++++--------------- R/dprhkdecop.R | 2 R/kdecop.R | 171 ++++++++++++++--------------- R/kdecopula-package.R | 92 +++++++-------- R/tll_functions.R | 14 +- README.md | 17 +- inst/README-unnamed-chunk-10-1.png |binary inst/README-unnamed-chunk-12-1.png |binary inst/README-unnamed-chunk-6-1.png |binary inst/README-unnamed-chunk-7-1.png |binary inst/README-unnamed-chunk-8-1.png |binary inst/README-unnamed-chunk-9-1.png |binary inst/include/evaluators.h | 1 inst/include/hfunc.h | 2 man/bw_bern.Rd | 3 man/bw_beta.Rd | 3 man/bw_mr.Rd | 3 man/bw_t.Rd | 3 man/bw_tll.Rd | 3 man/bw_tll_nn.Rd | 1 man/bw_tt_pi.Rd | 9 - man/dkdecop.Rd | 11 + man/hkdecop.Rd | 7 - man/kdecop.Rd | 95 ++++++++-------- man/kdecopula.Rd | 38 +++--- man/logLik.kdecopula.Rd | 7 - man/plot.kdecopula.Rd | 10 - man/wdbc.Rd | 3 src/RcppExports.cpp | 178 +++++++----------------------- src/evaluators.cpp | 1 src/hfunc.cpp | 1 src/init.c |only src/integrate.cpp | 70 +++++------- src/interp.cpp | 215 +++++++++++++++++-------------------- src/kernels.cpp | 75 +++++------- src/renorm.cpp | 61 ++++------ 41 files changed, 630 insertions(+), 927 deletions(-)
Title: Handy String and File Manipulation
Description: Handy string and file processing and manipulation tools. Built on
top of the functionality of 'stringr'. Good for those who like to do
all of their file and string manipulation from within R.
Author: Rory Nolan [aut, cre, cph],
Jim Hester [ctb],
Sergi Padilla-Parra [ths]
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between filesstrings versions 0.3.2 dated 2017-03-18 and 0.4.0 dated 2017-04-11
DESCRIPTION | 6 +-- MD5 | 38 +++++++++---------- NEWS.md | 19 ++++++--- R/RcppExports.R | 4 -- R/strings.R | 76 +++++++++++++++++++++----------------- R/utils.R | 16 ++++++-- README.md | 25 +++++++++--- inst/doc/files.R | 8 ++-- inst/doc/files.Rmd | 8 ++-- inst/doc/files.html | 21 ++++++---- inst/doc/strings.html | 4 +- man/AllEqual.Rd | 6 ++- man/ExtractNumbers.Rd | 38 +++++++++---------- man/GiveExt.Rd | 5 +- src/RcppExports.cpp | 12 ------ src/init.c | 2 - src/strings.cc | 6 --- tests/testthat/test_RcppExports.R | 2 - tests/testthat/test_strings.R | 3 + vignettes/files.Rmd | 8 ++-- 20 files changed, 165 insertions(+), 142 deletions(-)
Title: An Easy Way to Descriptive Analysis
Description:
Descriptive analysis is essential for publishing medical articles.
This package provides an easy way to conduct the descriptive analysis.
1. Both numeric and factor variables can be handled. For numeric variables, normality test will be applied to choose the parametric and nonparametric test.
2. Both two or more groups can be handled. For groups more than two, the post hoc test will be applied, 'Tukey' for the numeric variables and 'FDR' for the factor variables.
3. T test, ANOVA or Fisher test can be forced to apply.
Author: Zhicheng Du, Yuantao Hao
Maintainer: Zhicheng Du<dgdzc@hotmail.com>
Diff between easyDes versions 2.0 dated 2017-03-27 and 3.0 dated 2017-04-11
DESCRIPTION | 8 +-- MD5 | 6 +- R/eastDes.R | 140 ++++++++++++++++++--------------------------------------- man/easyDes.Rd | 16 ++++-- 4 files changed, 63 insertions(+), 107 deletions(-)
Title: Easy Pre and Post Assertions
Description: assertthat is an extension to stopifnot() that makes it
easy to declare the pre and post conditions that you code should
satisfy, while also producing friendly error messages so that your
users know what they've done wrong.
Author: Hadley Wickham [aut, cre]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between assertthat versions 0.1 dated 2013-12-05 and 0.2.0 dated 2017-04-11
assertthat-0.1/assertthat/inst |only assertthat-0.1/assertthat/tests/test-that.R |only assertthat-0.2.0/assertthat/DESCRIPTION | 18 ++++---- assertthat-0.2.0/assertthat/MD5 | 45 +++++++++++---------- assertthat-0.2.0/assertthat/NAMESPACE | 3 - assertthat-0.2.0/assertthat/R/assert-that.r | 20 ++++++--- assertthat-0.2.0/assertthat/R/assertions-file.r | 5 -- assertthat-0.2.0/assertthat/R/assertions-scalar.R | 6 +- assertthat-0.2.0/assertthat/R/assertions.r | 4 - assertthat-0.2.0/assertthat/R/validate-that.R | 4 - assertthat-0.2.0/assertthat/README.md | 14 +++++- assertthat-0.2.0/assertthat/man/are_equal.Rd | 15 ++----- assertthat-0.2.0/assertthat/man/assert-is.Rd | 13 ++---- assertthat-0.2.0/assertthat/man/assert_that.Rd | 45 ++++++++++++--------- assertthat-0.2.0/assertthat/man/assertions-file.Rd | 12 ++--- assertthat-0.2.0/assertthat/man/has_args.Rd | 15 +++---- assertthat-0.2.0/assertthat/man/has_attr.Rd | 11 ++--- assertthat-0.2.0/assertthat/man/noNA.Rd | 12 ++--- assertthat-0.2.0/assertthat/man/not_empty.Rd | 12 ++--- assertthat-0.2.0/assertthat/man/on_failure.Rd | 12 ++--- assertthat-0.2.0/assertthat/man/scalar.Rd | 27 +++++++----- assertthat-0.2.0/assertthat/man/validate_that.Rd | 19 +++++--- assertthat-0.2.0/assertthat/tests/testthat |only assertthat-0.2.0/assertthat/tests/testthat.R |only 24 files changed, 170 insertions(+), 142 deletions(-)
Title: Coding Sound Files for Use with NDL
Description: Make acoustic cues to use with the R packages 'ndl' or 'ndl2'. The package implements functions used
in the PLoS ONE paper:
Denis Arnold, Fabian Tomaschek, Konstantin Sering, Florence Lopez, and R. Harald Baayen (2017).
Words from spontaneous conversational speech can be recognized with human-like accuracy by
an error-driven learning algorithm that discriminates between meanings straight from smart
acoustic features, bypassing the phoneme as recognition unit. PLoS ONE 12(4):e0174623
https://doi.org/10.1371/journal.pone.0174623
More details can be found in the paper and the supplement.
'ndl' is available on CRAN. 'ndl2' is available by request from <konstantin.sering@uni-tuebingen.de>.
Author: Denis Arnold [aut, dtc, cre]
Maintainer: Denis Arnold <arnold@ids-mannheim.de>
Diff between AcousticNDLCodeR versions 1.0.0 dated 2017-03-17 and 1.0.1 dated 2017-04-11
DESCRIPTION | 19 ++++++++++--------- MD5 | 10 +++++----- R/AcousticNDLCodeR_package.R | 3 ++- R/word_classification_data.R | 7 ++++--- man/AcousticNDLCodeR.Rd | 3 ++- man/word_classification_data.Rd | 7 ++++--- 6 files changed, 27 insertions(+), 22 deletions(-)
More information about AcousticNDLCodeR at CRAN
Permanent link
Title: Visualization and Imputation of Missing Values
Description: New tools for the visualization of missing and/or imputed values
are introduced, which can be used for exploring the data and the structure of
the missing and/or imputed values. Depending on this structure of the missing
values, the corresponding methods may help to identify the mechanism generating
the missing values and allows to explore the data including missing values.
In addition, the quality of imputation can be visually explored using various
univariate, bivariate, multiple and multivariate plot methods. A graphical user
interface available in the separate package VIMGUI allows an easy handling of
the implemented plot methods.
Author: Matthias Templ, Andreas Alfons, Alexander Kowarik, Bernd Prantner
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between VIM versions 4.6.0 dated 2016-10-17 and 4.7.0 dated 2017-04-11
DESCRIPTION | 10 +++--- MD5 | 27 ++++++++-------- NAMESPACE | 2 - NEWS | 2 + R/colSequence.R | 10 ++---- R/hotdeck.R | 33 ++++++++++++++------ R/irmi.R | 77 ++++++++++++++++++++++++++++++++++++------------ R/kNNFaster.R | 12 +++---- R/matrixplot.R | 25 +++++---------- man/colSequence.Rd | 7 +--- man/irmi.Rd | 5 +++ man/matrixplot.Rd | 4 -- src/gowerD.cpp | 5 +++ tests/test_data_frame.R | 3 - tests/test_impNA.R |only 15 files changed, 138 insertions(+), 84 deletions(-)
Title: Split-Population Duration (Cure) Regression
Description: An implementation of split-population duration regression models.
Unlike regular duration models, split-population duration models are
mixture models that accommodate the presence of a sub-population that is
not at risk for failure, e.g. cancer patients who have been cured by
treatment. This package implements Weibull and Loglogistic forms for the
duration component, and focuses on data with time-varying covariates.
These models were originally formulated in Boag (1949)
<http://www.jstor.org/stable/2983694> and Berkson and Gage (1952)
<http://www.jstor.org/stable/2281318>, and extended in Schmidt and Witte
(1989) <doi:10.1016/0304-4076(89)90034-1>.
Author: Andreas Beger [aut, cre],
Daina Chiba [aut],
Daniel W. Hill, Jr. [aut],
Nils W. Metternich [aut],
Shahryar Minhas [aut],
Michael D. Ward [aut, cph]
Maintainer: Andreas Beger <adbeger@gmail.com>
Diff between spduration versions 0.15.1 dated 2016-05-12 and 0.16.0 dated 2017-04-11
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Title: Spatial Analysis and Modelling
Description: Utilities to support spatial data manipulation, query, sampling
and modelling. Functions include models for species population density, download
utilities for climate and global deforestation spatial products, spatial
smoothing, multivariate separability, point process model for creating pseudo-
absences and sub-sampling, polygon and point-distance landscape metrics,
auto-logistic model, sampling models, cluster optimization and statistical
exploratory tools.
Author: Jeffrey S. Evans [aut, cre],
Karthik Ram [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
Diff between spatialEco versions 0.1-5 dated 2016-06-14 and 0.1-7 dated 2017-04-11
spatialEco-0.1-5/spatialEco/R/trig.trans.R |only spatialEco-0.1-5/spatialEco/man/mwCorr.Rd |only spatialEco-0.1-5/spatialEco/man/trig.trans.Rd |only spatialEco-0.1-7/spatialEco/DESCRIPTION | 16 - spatialEco-0.1-7/spatialEco/MD5 | 201 ++++++++------ spatialEco-0.1-7/spatialEco/NAMESPACE | 20 + spatialEco-0.1-7/spatialEco/R/curvature.R |only spatialEco-0.1-7/spatialEco/R/daymet.point.R | 2 spatialEco-0.1-7/spatialEco/R/dissection.R |only spatialEco-0.1-7/spatialEco/R/download.daymet.R | 33 +- spatialEco-0.1-7/spatialEco/R/elev-data.R |only spatialEco-0.1-7/spatialEco/R/hli.R |only spatialEco-0.1-7/spatialEco/R/hsp.R |only spatialEco-0.1-7/spatialEco/R/idw.smoothing.R | 2 spatialEco-0.1-7/spatialEco/R/insert.values.R | 21 - spatialEco-0.1-7/spatialEco/R/kde2D.R |only spatialEco-0.1-7/spatialEco/R/land.metrics.R | 4 spatialEco-0.1-7/spatialEco/R/logistic.regression.R | 4 spatialEco-0.1-7/spatialEco/R/mwCorr.R | 3 spatialEco-0.1-7/spatialEco/R/outliers.R | 18 - spatialEco-0.1-7/spatialEco/R/pp.subsample.R | 10 spatialEco-0.1-7/spatialEco/R/pseudo.absence.R | 10 spatialEco-0.1-7/spatialEco/R/raster.Zscore.R |only spatialEco-0.1-7/spatialEco/R/raster.deviation.R |only spatialEco-0.1-7/spatialEco/R/raster.entropy.R | 80 +++-- spatialEco-0.1-7/spatialEco/R/raster.gaussian.smooth.R |only spatialEco-0.1-7/spatialEco/R/raster.invert.R |only spatialEco-0.1-7/spatialEco/R/raster.mds.R |only spatialEco-0.1-7/spatialEco/R/raster.moments.R |only spatialEco-0.1-7/spatialEco/R/raster.transformations.R |only spatialEco-0.1-7/spatialEco/R/sa.trans.R |only spatialEco-0.1-7/spatialEco/R/sar.R |only spatialEco-0.1-7/spatialEco/R/sobel.R |only spatialEco-0.1-7/spatialEco/R/srr.R |only spatialEco-0.1-7/spatialEco/R/tpi.R | 21 - 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spatialEco-0.1-7/spatialEco/man/trasp.Rd |only spatialEco-0.1-7/spatialEco/man/trend.line.Rd | 1 spatialEco-0.1-7/spatialEco/man/tri.Rd | 18 - spatialEco-0.1-7/spatialEco/man/vrm.Rd | 9 spatialEco-0.1-7/spatialEco/man/wt.centroid.Rd | 1 spatialEco-0.1-7/spatialEco/man/zonal.stats.Rd | 1 122 files changed, 425 insertions(+), 363 deletions(-)
Title: Indoor Positioning Fingerprinting Toolset
Description: Algorithms and utility functions for indoor positioning using fingerprinting techniques.
These functions are designed for manipulation of RSSI (Received Signal Strength Intensity) data
sets, estimation of positions,comparison of the performance of different models, and graphical
visualization of data. Machine learning algorithms and methods such as k-nearest neighbors or
probabilistic fingerprinting are implemented in this package to perform analysis
and estimations over RSSI data sets.
Author: Emilio Sansano
Maintainer: Emilio Sansano <esansano@uji.es>
Diff between ipft versions 0.3.1 dated 2017-03-15 and 0.5 dated 2017-04-11
DESCRIPTION | 6 MD5 | 26 - NAMESPACE | 2 R/ipft.R | 690 +++++++++++++++++++++++++++++++++-------------------- man/ipfEstbp.Rd | 8 man/ipfEstimate.Rd | 22 - man/ipfKnn.Rd | 23 - man/ipfPlotEcdf.Rd | 7 man/ipfPlotEst.Rd | 8 man/ipfPlotLoc.Rd | 4 man/ipfPlotPdf.Rd | 7 man/ipfProb.Rd | 27 +- man/ipfProx.Rd | 17 - src/ipf.cpp | 2 14 files changed, 519 insertions(+), 330 deletions(-)
Title: Computationally Efficient Queue Simulation
Description: Implementation of a computationally efficient method for
simulating queues with arbitrary arrival and service times.
Author: Anthony Ebert [aut, cre]
Maintainer: Anthony Ebert <anthonyebert+CRAN@gmail.com>
Diff between queuecomputer versions 0.6.1 dated 2016-12-20 and 0.8.1 dated 2017-04-11
queuecomputer-0.6.1/queuecomputer/man/print.summary_queue_df.Rd |only queuecomputer-0.6.1/queuecomputer/man/summary.queue_df.Rd |only queuecomputer-0.8.1/queuecomputer/DESCRIPTION | 10 queuecomputer-0.8.1/queuecomputer/MD5 | 60 +- queuecomputer-0.8.1/queuecomputer/NAMESPACE | 16 queuecomputer-0.8.1/queuecomputer/NEWS.md | 8 queuecomputer-0.8.1/queuecomputer/R/core_queuefunctions.R | 233 ++++++---- queuecomputer-0.8.1/queuecomputer/R/dplyr_plugins.R |only queuecomputer-0.8.1/queuecomputer/R/plot_functions.R |only queuecomputer-0.8.1/queuecomputer/R/post_analysis.R | 202 +++++--- queuecomputer-0.8.1/queuecomputer/R/utils.R | 57 ++ queuecomputer-0.8.1/queuecomputer/R/zzz.R |only queuecomputer-0.8.1/queuecomputer/README.md | 153 ++---- queuecomputer-0.8.1/queuecomputer/build/vignette.rds |binary queuecomputer-0.8.1/queuecomputer/inst/doc/Howto.R | 51 +- queuecomputer-0.8.1/queuecomputer/inst/doc/Howto.Rmd | 53 +- queuecomputer-0.8.1/queuecomputer/inst/doc/Howto.html | 123 ++--- queuecomputer-0.8.1/queuecomputer/inst/doc/MMk_queues.R | 51 +- queuecomputer-0.8.1/queuecomputer/inst/doc/MMk_queues.Rmd | 51 +- queuecomputer-0.8.1/queuecomputer/inst/doc/MMk_queues.html | 180 ++++--- queuecomputer-0.8.1/queuecomputer/man/average_queue.Rd |only queuecomputer-0.8.1/queuecomputer/man/create_batches.Rd |only queuecomputer-0.8.1/queuecomputer/man/depart.Rd |only queuecomputer-0.8.1/queuecomputer/man/lag_step.Rd | 16 queuecomputer-0.8.1/queuecomputer/man/plot.queue_list.Rd |only queuecomputer-0.8.1/queuecomputer/man/print.queue_list.Rd |only queuecomputer-0.8.1/queuecomputer/man/print.summary_queue_list.Rd |only queuecomputer-0.8.1/queuecomputer/man/ql_summary.Rd |only queuecomputer-0.8.1/queuecomputer/man/queue.Rd | 25 - queuecomputer-0.8.1/queuecomputer/man/queue_lengths.Rd |only queuecomputer-0.8.1/queuecomputer/man/queue_step.Rd | 77 +-- queuecomputer-0.8.1/queuecomputer/man/summary.queue_list.Rd |only queuecomputer-0.8.1/queuecomputer/man/wait_step.Rd | 12 queuecomputer-0.8.1/queuecomputer/src/init.c |only queuecomputer-0.8.1/queuecomputer/tests/create_batch_test.RData |only queuecomputer-0.8.1/queuecomputer/tests/queue_length_obj.RData |only queuecomputer-0.8.1/queuecomputer/tests/testthat/test_addons.R |only queuecomputer-0.8.1/queuecomputer/tests/testthat/test_deterministic.R | 76 +-- queuecomputer-0.8.1/queuecomputer/vignettes/Howto.Rmd | 53 +- queuecomputer-0.8.1/queuecomputer/vignettes/MMk_queues.Rmd | 51 +- 40 files changed, 939 insertions(+), 619 deletions(-)
Title: R-Based API for Accessing the MSKCC Cancer Genomics Data Server
(CGDS)
Description: Provides a basic set of R functions for querying the Cancer
Genomics Data Server (CGDS), hosted by the Computational Biology Center at
Memorial-Sloan-Kettering Cancer Center (MSKCC).
Author: Anders Jacobsen <jacobsen@cbio.mskcc.org>
Maintainer: Augustin Luna <lunaa@cbio.mskcc.org>
Diff between cgdsr versions 1.2.5 dated 2015-08-27 and 1.2.6 dated 2017-04-11
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- build/vignette.rds |binary inst/doc/cgdsr.pdf |binary 4 files changed, 7 insertions(+), 7 deletions(-)
Title: Cognitive Diagnosis Modeling
Description:
Functions for cognitive diagnosis modeling
and multidimensional item response modeling for
dichotomous and polytomous data. This package
enables the estimation of the DINA and DINO model,
the multiple group (polytomous) GDINA model,
the multiple choice DINA model, the general diagnostic
model (GDM), the multidimensional linear compensatory
item response model and the structured latent class
model (SLCA).
Author:
Alexander Robitzsch [aut, cre], Thomas Kiefer [aut],
Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between CDM versions 5.4-0 dated 2017-02-08 and 5.5-21 dated 2017-04-11
CDM-5.4-0/CDM/R/mad_aux.R |only CDM-5.4-0/CDM/R/md_aux.R |only CDM-5.4-0/CDM/R/rmsea_aux.R |only CDM-5.5-21/CDM/DESCRIPTION | 8 CDM-5.5-21/CDM/MD5 | 28 CDM-5.5-21/CDM/R/IRT.RMSD.R | 28 CDM-5.5-21/CDM/R/IRT_RMSD_calc_distributions.R |only CDM-5.5-21/CDM/R/IRT_RMSD_calc_rmsd.R |only CDM-5.5-21/CDM/R/IRT_RMSD_proc_dist_item.R |only CDM-5.5-21/CDM/R/array3_sum.R |only CDM-5.5-21/CDM/R/itemfit.sx2.R | 5 CDM-5.5-21/CDM/R/itemfit.sx2_aux.R | 15 CDM-5.5-21/CDM/R/replace_NA.R |only CDM-5.5-21/CDM/R/summary.IRT.RMSD.R | 6 CDM-5.5-21/CDM/R/zzz.R | 2 CDM-5.5-21/CDM/inst/NEWS | 1277 ++++++++++++------------- CDM-5.5-21/CDM/man/CDM-package.Rd | 94 - CDM-5.5-21/CDM/man/IRT.RMSD.Rd | 2 CDM-5.5-21/CDM/man/skillspace.hierarchy.Rd | 3 19 files changed, 751 insertions(+), 717 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 <stevescott@google.com>
Maintainer: Steven L. Scott <stevescott@google.com>
Diff between bsts versions 0.6.5 dated 2016-08-18 and 0.7.0 dated 2017-04-11
bsts-0.6.5/bsts/man/add.generalized.local.linear.trend.Rd |only bsts-0.6.5/bsts/man/bsts.holdout.prediction.errors.Rd |only bsts-0.7.0/bsts/DESCRIPTION | 14 bsts-0.7.0/bsts/MD5 | 85 +-- bsts-0.7.0/bsts/NAMESPACE | 96 +++ bsts-0.7.0/bsts/R/add.ar.R | 126 ++++ bsts-0.7.0/bsts/R/add.generalized.local.linear.trend.R | 124 ---- bsts-0.7.0/bsts/R/add.semilocal.linear.trend.R |only bsts-0.7.0/bsts/R/add.trig.R | 4 bsts-0.7.0/bsts/R/bsts.R | 314 +++++++----- bsts-0.7.0/bsts/R/compare.bsts.models.R | 19 bsts-0.7.0/bsts/R/diagnostics.R | 103 +-- bsts-0.7.0/bsts/R/format.learning.data.R | 25 bsts-0.7.0/bsts/R/format.timestamps.R |only bsts-0.7.0/bsts/R/plot.holidays.R | 2 bsts-0.7.0/bsts/R/plot_seasonal_effect.R | 2 bsts-0.7.0/bsts/R/plots.R | 69 ++ bsts-0.7.0/bsts/R/predict.bsts.R | 3 bsts-0.7.0/bsts/R/utils.R | 5 bsts-0.7.0/bsts/man/MATCH.NumericTimestamps.Rd |only bsts-0.7.0/bsts/man/add.ar.Rd | 2 bsts-0.7.0/bsts/man/add.dynamic.regression.Rd | 8 bsts-0.7.0/bsts/man/add.semilocal.linear.trend.Rd |only bsts-0.7.0/bsts/man/auto.ar.Rd |only bsts-0.7.0/bsts/man/bsts.Rd | 187 +++++-- bsts-0.7.0/bsts/man/bsts.options.Rd |only bsts-0.7.0/bsts/man/compare.bsts.models.Rd | 4 bsts-0.7.0/bsts/man/format.timestamps.Rd |only bsts-0.7.0/bsts/man/geometric.sequence.Rd |only bsts-0.7.0/bsts/man/one.step.prediction.errors.Rd | 17 bsts-0.7.0/bsts/man/plot.bsts.Rd | 19 bsts-0.7.0/bsts/man/regularize.timestamps.Rd |only bsts-0.7.0/bsts/man/spike.slab.ar.prior.Rd |only bsts-0.7.0/bsts/src/aggregate_time_series.cc | 6 bsts-0.7.0/bsts/src/bsts.cc | 5 bsts-0.7.0/bsts/src/bsts_init.cc |only bsts-0.7.0/bsts/src/mixed_frequency.cc | 56 -- bsts-0.7.0/bsts/src/model_manager.cc | 34 - bsts-0.7.0/bsts/src/model_manager.h | 38 + bsts-0.7.0/bsts/src/state_space_gaussian_model_manager.cc | 23 bsts-0.7.0/bsts/src/state_space_gaussian_model_manager.h | 4 bsts-0.7.0/bsts/src/state_space_logit_model_manager.cc | 39 + bsts-0.7.0/bsts/src/state_space_logit_model_manager.h | 4 bsts-0.7.0/bsts/src/state_space_poisson_model_manager.cc | 43 + bsts-0.7.0/bsts/src/state_space_poisson_model_manager.h | 4 bsts-0.7.0/bsts/src/state_space_regression_model_manager.cc | 33 + bsts-0.7.0/bsts/src/state_space_student_model_manager.cc | 35 + bsts-0.7.0/bsts/src/state_space_student_model_manager.h | 4 bsts-0.7.0/bsts/src/utils.cc | 2 bsts-0.7.0/bsts/src/utils.h | 4 50 files changed, 990 insertions(+), 572 deletions(-)
Title: Business Days Calculations and Utilities
Description: Business days calculations based on a list of holidays and
nonworking weekdays. Quite useful for fixed income and derivatives pricing.
Author: Wilson Freitas <wilson.freitas@gmail.com>
Maintainer: Wilson Freitas <wilson.freitas@gmail.com>
Diff between bizdays versions 1.0.1 dated 2016-09-13 and 1.0.2 dated 2017-04-11
bizdays-1.0.1/bizdays/inst/tests |only bizdays-1.0.2/bizdays/DESCRIPTION | 10 - bizdays-1.0.2/bizdays/LICENSE | 2 bizdays-1.0.2/bizdays/MD5 | 55 +++++----- bizdays-1.0.2/bizdays/NAMESPACE | 1 bizdays-1.0.2/bizdays/NEWS | 12 ++ bizdays-1.0.2/bizdays/R/bizdays.R | 4 bizdays-1.0.2/bizdays/R/calendar.R | 44 ++++++-- bizdays-1.0.2/bizdays/R/create-calendars.R | 8 + bizdays-1.0.2/bizdays/R/offset.R | 10 - bizdays-1.0.2/bizdays/build/vignette.rds |binary bizdays-1.0.2/bizdays/inst/doc/Creating_Calendars.html | 13 +- bizdays-1.0.2/bizdays/inst/doc/Setting_default_calendar_in_Rprofile.html | 13 +- bizdays-1.0.2/bizdays/man/adjust.date.Rd | 8 - bizdays-1.0.2/bizdays/man/bizdays-package.Rd | 1 bizdays-1.0.2/bizdays/man/bizdays.Rd | 2 bizdays-1.0.2/bizdays/man/bizdays.options.Rd | 1 bizdays-1.0.2/bizdays/man/bizdayse.Rd | 2 bizdays-1.0.2/bizdays/man/bizseq.Rd | 2 bizdays-1.0.2/bizdays/man/calendar-register.Rd | 5 bizdays-1.0.2/bizdays/man/create.calendar.Rd | 3 bizdays-1.0.2/bizdays/man/holidaysANBIMA.Rd | 1 bizdays-1.0.2/bizdays/man/is.bizday.Rd | 2 bizdays-1.0.2/bizdays/man/offset.Rd | 4 bizdays-1.0.2/bizdays/man/other-calendars.Rd | 4 bizdays-1.0.2/bizdays/tests |only 26 files changed, 130 insertions(+), 77 deletions(-)
Title: Summaries and Population Structure Analyses of Genetic Data
Description: A toolkit for analyzing stratified population genetic data.
Functions are provided for summarizing and checking loci
(haploid, diploid, and polyploid), single stranded DNA sequences,
calculating most population subdivision metrics, and running external programs
such as structure and fastsimcoal. The package is further described in
Archer et al (2016) <doi:10.1111/1755-0998.12559>.
Author: Eric Archer [aut, cre],
Paula Adams [aut],
Brita Schneiders [aut],
Sarina Fernandez [aut],
Warren Asfazadour [aut]
Maintainer: Eric Archer <eric.archer@noaa.gov>
Diff between strataG versions 1.0.5 dated 2016-05-31 and 2.0.2 dated 2017-04-11
strataG-1.0.5/strataG/R/Hstats.R |only strataG-1.0.5/strataG/R/expectedNumAlleles.R |only strataG-1.0.5/strataG/R/fstToNm.R |only strataG-1.0.5/strataG/R/haplotypeLikelihoods.R |only strataG-1.0.5/strataG/R/idRows.R |only strataG-1.0.5/strataG/R/numGensEq.R |only strataG-1.0.5/strataG/R/statChi2.R |only strataG-1.0.5/strataG/R/statFis.R |only strataG-1.0.5/strataG/R/statFst.R |only strataG-1.0.5/strataG/R/statGst.R |only strataG-1.0.5/strataG/R/statJostD.R |only strataG-1.0.5/strataG/R/statPhist.R |only strataG-1.0.5/strataG/R/wrightFst.R |only strataG-1.0.5/strataG/R/write.arlequin.R |only strataG-1.0.5/strataG/man/expectedNumAlleles.Rd |only strataG-1.0.5/strataG/man/fstToNm.Rd |only strataG-1.0.5/strataG/man/haplotypeLikelihoods.Rd |only strataG-1.0.5/strataG/man/idRows.Rd |only strataG-1.0.5/strataG/man/numGensEq.Rd |only strataG-1.0.5/strataG/man/wrightFst.Rd |only strataG-1.0.5/strataG/man/write.arlequin.Rd |only strataG-2.0.2/strataG/DESCRIPTION | 73 +- strataG-2.0.2/strataG/MD5 | 410 ++++++++------- strataG-2.0.2/strataG/NAMESPACE | 53 + strataG-2.0.2/strataG/R/RcppExports.R | 82 --- strataG-2.0.2/strataG/R/alleleFreqFormat.R | 2 strataG-2.0.2/strataG/R/alleleFreqs.R | 31 - strataG-2.0.2/strataG/R/allelicRichness.R | 7 strataG-2.0.2/strataG/R/arlequin.R |only strataG-2.0.2/strataG/R/as.array.gtypes.R |only strataG-2.0.2/strataG/R/as.data.frame.gtypes.R | 18 strataG-2.0.2/strataG/R/as.matrix.gtypes.R | 61 +- strataG-2.0.2/strataG/R/clumpp.R | 4 strataG-2.0.2/strataG/R/df2gtypes.R | 1 strataG-2.0.2/strataG/R/dupGenotypes.R | 12 strataG-2.0.2/strataG/R/evanno.R | 91 +-- strataG-2.0.2/strataG/R/expandHaplotypes.R |only strataG-2.0.2/strataG/R/fasta.R | 2 strataG-2.0.2/strataG/R/fastsimcoal.R | 44 + strataG-2.0.2/strataG/R/freq2GenData.R | 4 strataG-2.0.2/strataG/R/fusFs.R | 37 - strataG-2.0.2/strataG/R/gelato.R | 219 ++++---- strataG-2.0.2/strataG/R/genepop.R | 31 - strataG-2.0.2/strataG/R/gtypes.accessors.R | 183 +++--- strataG-2.0.2/strataG/R/gtypes.class.R | 93 +-- strataG-2.0.2/strataG/R/gtypes2genind.R | 3 strataG-2.0.2/strataG/R/heterozygosity.R | 16 strataG-2.0.2/strataG/R/initialize.gtypes.R | 84 +-- strataG-2.0.2/strataG/R/is.gtypes.R | 5 strataG-2.0.2/strataG/R/jackHWE.R | 26 strataG-2.0.2/strataG/R/labelHaplotypes.R | 163 +++-- strataG-2.0.2/strataG/R/ldNe.R |only strataG-2.0.2/strataG/R/lowFreqSubs.R | 11 strataG-2.0.2/strataG/R/maf.R |only strataG-2.0.2/strataG/R/maverickRun.R |only strataG-2.0.2/strataG/R/neiDa.R | 20 strataG-2.0.2/strataG/R/nucleotideDivergence.R | 9 strataG-2.0.2/strataG/R/numAlleles.R | 7 strataG-2.0.2/strataG/R/numGenotyped.R |only strataG-2.0.2/strataG/R/numMissing.R | 9 strataG-2.0.2/strataG/R/numericSNPmat.R |only strataG-2.0.2/strataG/R/phase.R | 16 strataG-2.0.2/strataG/R/popGenEqns.R |only strataG-2.0.2/strataG/R/popStructStat.R | 272 ++++++++- strataG-2.0.2/strataG/R/popStructTest.R | 82 --- strataG-2.0.2/strataG/R/privateAlleles.R | 1 strataG-2.0.2/strataG/R/propUniqueAlleles.R | 9 strataG-2.0.2/strataG/R/qaqc.R | 32 - strataG-2.0.2/strataG/R/removeSequences.R | 6 strataG-2.0.2/strataG/R/sequenceLikelihoods.R |only strataG-2.0.2/strataG/R/sharedLoci.R | 41 - strataG-2.0.2/strataG/R/show.gtypes.R | 4 strataG-2.0.2/strataG/R/strataG-internal.R | 44 + strataG-2.0.2/strataG/R/strataGUI.R |only strataG-2.0.2/strataG/R/strataSplit.R | 4 strataG-2.0.2/strataG/R/stratify.R | 20 strataG-2.0.2/strataG/R/structure.R | 39 - strataG-2.0.2/strataG/R/structurePlot.R | 33 - strataG-2.0.2/strataG/R/summarizeLoci.R | 12 strataG-2.0.2/strataG/R/summarizeSamples.R |only strataG-2.0.2/strataG/R/summary.gtypes.R | 113 ++-- strataG-2.0.2/strataG/R/theta.R | 3 strataG-2.0.2/strataG/R/write.nexus.snapp.R | 18 strataG-2.0.2/strataG/README.md | 74 ++ strataG-2.0.2/strataG/build/vignette.rds |binary strataG-2.0.2/strataG/data/dloop.g.rda |binary strataG-2.0.2/strataG/data/dolph.haps.rda |binary strataG-2.0.2/strataG/data/dolph.msats.rda |binary strataG-2.0.2/strataG/data/dolph.seqs.rda |binary strataG-2.0.2/strataG/data/dolph.strata.rda |binary strataG-2.0.2/strataG/data/msats.g.rda |binary strataG-2.0.2/strataG/inst/CITATION |only strataG-2.0.2/strataG/inst/doc/external.programs.Rmd | 2 strataG-2.0.2/strataG/inst/doc/external.programs.html | 15 strataG-2.0.2/strataG/inst/doc/gtypes.R | 11 strataG-2.0.2/strataG/inst/doc/gtypes.Rmd | 25 strataG-2.0.2/strataG/inst/doc/gtypes.html | 283 +++++----- strataG-2.0.2/strataG/inst/doc/population.structure.html | 43 - strataG-2.0.2/strataG/inst/doc/qaqc.R | 3 strataG-2.0.2/strataG/inst/doc/qaqc.Rmd | 7 strataG-2.0.2/strataG/inst/doc/qaqc.html | 172 +++--- strataG-2.0.2/strataG/inst/doc/sequences.R | 11 strataG-2.0.2/strataG/inst/doc/sequences.Rmd | 11 strataG-2.0.2/strataG/inst/doc/sequences.html | 101 ++- strataG-2.0.2/strataG/inst/doc/summaries.Rmd | 2 strataG-2.0.2/strataG/inst/doc/summaries.html | 17 strataG-2.0.2/strataG/inst/shiny |only strataG-2.0.2/strataG/man/LDgenepop.Rd | 7 strataG-2.0.2/strataG/man/TiTvRatio.Rd | 3 strataG-2.0.2/strataG/man/alleleFreqFormat.Rd | 7 strataG-2.0.2/strataG/man/alleleFreqs.Rd | 16 strataG-2.0.2/strataG/man/alleleSplit.Rd | 1 strataG-2.0.2/strataG/man/allelicRichness.Rd | 1 strataG-2.0.2/strataG/man/arlequin.Rd |only strataG-2.0.2/strataG/man/as.array.gtypes.Rd |only strataG-2.0.2/strataG/man/as.data.frame.gtypes.Rd | 18 strataG-2.0.2/strataG/man/as.matrix-gtypes-method.Rd | 16 strataG-2.0.2/strataG/man/as.multidna.Rd | 7 strataG-2.0.2/strataG/man/baseFreqs.Rd | 1 strataG-2.0.2/strataG/man/bowhead.snp.position.Rd | 1 strataG-2.0.2/strataG/man/bowhead.snps.Rd | 1 strataG-2.0.2/strataG/man/clumpp.Rd | 7 strataG-2.0.2/strataG/man/createConsensus.Rd | 1 strataG-2.0.2/strataG/man/df2gtypes.Rd | 7 strataG-2.0.2/strataG/man/dloop.g.Rd | 1 strataG-2.0.2/strataG/man/dolph.haps.Rd | 1 strataG-2.0.2/strataG/man/dolph.msats.Rd | 1 strataG-2.0.2/strataG/man/dolph.seqs.Rd | 1 strataG-2.0.2/strataG/man/dolph.strata.Rd | 1 strataG-2.0.2/strataG/man/dupGenotypes.Rd | 8 strataG-2.0.2/strataG/man/evanno.Rd | 15 strataG-2.0.2/strataG/man/expandHaplotypes.Rd |only strataG-2.0.2/strataG/man/fasta.Rd | 1 strataG-2.0.2/strataG/man/fastsimcoal.Rd | 18 strataG-2.0.2/strataG/man/fastsimcoal.input.Rd | 11 strataG-2.0.2/strataG/man/fixedDifferences.Rd | 7 strataG-2.0.2/strataG/man/fixedSites.Rd | 7 strataG-2.0.2/strataG/man/freq2GenData.Rd | 1 strataG-2.0.2/strataG/man/fusFs.Rd | 16 strataG-2.0.2/strataG/man/gelato.Rd | 15 strataG-2.0.2/strataG/man/genepop.Rd | 7 strataG-2.0.2/strataG/man/gtypes-class.Rd | 31 - strataG-2.0.2/strataG/man/gtypes.accessors.Rd | 92 +-- strataG-2.0.2/strataG/man/gtypes2genind.Rd | 9 strataG-2.0.2/strataG/man/gtypes2loci.Rd | 7 strataG-2.0.2/strataG/man/gtypes2phyDat.Rd | 7 strataG-2.0.2/strataG/man/heterozygosity.Rd | 7 strataG-2.0.2/strataG/man/hweTest.Rd | 11 strataG-2.0.2/strataG/man/initialize-gtypes-method.Rd | 7 strataG-2.0.2/strataG/man/is.gtypes.Rd | 1 strataG-2.0.2/strataG/man/iupacCode.Rd | 7 strataG-2.0.2/strataG/man/jackHWE.Rd | 9 strataG-2.0.2/strataG/man/labelHaplotypes.Rd | 40 - strataG-2.0.2/strataG/man/ldNe.Rd |only strataG-2.0.2/strataG/man/lowFreqSubs.Rd | 1 strataG-2.0.2/strataG/man/mRatio.Rd | 7 strataG-2.0.2/strataG/man/maf.Rd |only strataG-2.0.2/strataG/man/mafft.Rd | 7 strataG-2.0.2/strataG/man/maverickRun.Rd |only strataG-2.0.2/strataG/man/mega.Rd | 11 strataG-2.0.2/strataG/man/mostDistantSequences.Rd | 1 strataG-2.0.2/strataG/man/mostRepresentativeSequences.Rd | 1 strataG-2.0.2/strataG/man/msats.g.Rd | 1 strataG-2.0.2/strataG/man/neiDa.Rd | 7 strataG-2.0.2/strataG/man/nucleotideDivergence.Rd | 9 strataG-2.0.2/strataG/man/nucleotideDiversity.Rd | 1 strataG-2.0.2/strataG/man/numAlleles.Rd | 6 strataG-2.0.2/strataG/man/numGenotyped.Rd |only strataG-2.0.2/strataG/man/numMissing.Rd | 1 strataG-2.0.2/strataG/man/numericSNPmat.Rd |only strataG-2.0.2/strataG/man/permuteStrata.Rd | 1 strataG-2.0.2/strataG/man/phase.Rd | 13 strataG-2.0.2/strataG/man/popGenEqns.Rd |only strataG-2.0.2/strataG/man/popStructStat.Rd | 37 - strataG-2.0.2/strataG/man/popStructTest.Rd | 35 - strataG-2.0.2/strataG/man/privateAlleles.Rd | 7 strataG-2.0.2/strataG/man/propUniqueAlleles.Rd | 12 strataG-2.0.2/strataG/man/qaqc.Rd | 10 strataG-2.0.2/strataG/man/readGenData.Rd | 1 strataG-2.0.2/strataG/man/removeSequences.Rd | 4 strataG-2.0.2/strataG/man/sequence2gtypes.Rd | 1 strataG-2.0.2/strataG/man/sequenceLikelihoods.Rd |only strataG-2.0.2/strataG/man/sharedLoci.Rd | 18 strataG-2.0.2/strataG/man/show-gtypes-method.Rd | 1 strataG-2.0.2/strataG/man/simGammaHaps.Rd | 1 strataG-2.0.2/strataG/man/strataG-internal.Rd | 20 strataG-2.0.2/strataG/man/strataG-package.Rd | 3 strataG-2.0.2/strataG/man/strataGUI.Rd |only strataG-2.0.2/strataG/man/strataSplit.Rd | 1 strataG-2.0.2/strataG/man/stratify.Rd | 7 strataG-2.0.2/strataG/man/structure.Rd | 11 strataG-2.0.2/strataG/man/structurePlot.Rd | 14 strataG-2.0.2/strataG/man/summarizeLoci.Rd | 1 strataG-2.0.2/strataG/man/summarizeSamples.Rd |only strataG-2.0.2/strataG/man/summarizeSeqs.Rd | 1 strataG-2.0.2/strataG/man/summary-gtypes-method.Rd | 5 strataG-2.0.2/strataG/man/tajimasD.Rd | 7 strataG-2.0.2/strataG/man/theta.Rd | 1 strataG-2.0.2/strataG/man/trimNs.Rd | 1 strataG-2.0.2/strataG/man/validIupacCodes.Rd | 1 strataG-2.0.2/strataG/man/variableSites.Rd | 7 strataG-2.0.2/strataG/man/write.gtypes.Rd | 1 strataG-2.0.2/strataG/man/write.nexus.snapp.Rd | 1 strataG-2.0.2/strataG/src/Hstats_C.cpp | 74 +- strataG-2.0.2/strataG/src/RcppExports.cpp | 352 ++++-------- strataG-2.0.2/strataG/src/init.c |only strataG-2.0.2/strataG/src/misc.funcs.cpp | 66 +- strataG-2.0.2/strataG/src/statChi2_C.cpp | 5 strataG-2.0.2/strataG/src/statFis_C.cpp | 6 strataG-2.0.2/strataG/src/statFst_C.cpp | 71 +- strataG-2.0.2/strataG/src/statGst_C.cpp | 22 strataG-2.0.2/strataG/src/statJostD_C.cpp | 9 strataG-2.0.2/strataG/src/statPhist_C.cpp | 3 strataG-2.0.2/strataG/tests |only strataG-2.0.2/strataG/vignettes/gtypes.Rmd | 5 strataG-2.0.2/strataG/vignettes/qaqc.Rmd | 7 strataG-2.0.2/strataG/vignettes/sequences.Rmd | 11 217 files changed, 2551 insertions(+), 2126 deletions(-)
Title: Collection of Convenient Functions for Common Statistical
Computations
Description: Collection of convenient functions for common statistical computations,
which are not directly provided by R's base or stats packages.
This package aims at providing, first, shortcuts for statistical
measures, which otherwise could only be calculated with additional
effort (like standard errors or root mean squared errors). Second,
these shortcut functions are generic (if appropriate), and can be
applied not only to vectors, but also to other objects as well
(e.g., the Coefficient of Variation can be computed for vectors,
linear models, or linear mixed models; the r2()-function returns
the r-squared value for 'lm', 'glm', 'merMod' or 'lme' objects).
The focus of most functions lies on summary statistics or fit
measures for regression models, including generalized linear
models and mixed effects models. However, some of the functions
also deal with other statistical measures, like Cronbach's Alpha,
Cramer's V, Phi etc.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjstats versions 0.9.0 dated 2017-03-06 and 0.10.0 dated 2017-04-11
DESCRIPTION | 18 - MD5 | 112 +++---- NAMESPACE | 359 ++++++++++++----------- NEWS | 12 NEWS.md | 14 R/S3-methods.R | 726 ++++++++++++++++++++++++++--------------------- R/cv_error.R |only R/helpfunctions.R | 1 R/icc.R | 5 R/internal_consistency.R | 526 +++++++++++++++++----------------- R/odds_to_rr.R | 174 ++++++----- R/predictive_accuracy.R | 32 +- R/prop.R | 83 ++++- R/rmse.R | 4 R/se.R | 23 + R/sum.R |only R/svyglmnb.R | 232 ++++++++------- README.md | 96 +++--- build/partial.rdb |binary man/boot_ci.Rd | 246 +++++++-------- man/bootstrap.Rd | 160 +++++----- man/check_assumptions.Rd | 282 +++++++++--------- man/chisq_gof.Rd | 118 +++---- man/cod.Rd | 90 ++--- man/converge_ok.Rd | 104 +++--- man/cv.Rd | 122 +++---- man/cv_error.Rd |only man/deff.Rd | 84 ++--- man/efc.Rd | 66 ++-- man/eta_sq.Rd | 84 ++--- man/get_model_pval.Rd | 108 +++--- man/hoslem_gof.Rd | 86 ++--- man/icc.Rd | 247 ++++++++------- man/inequ_trend.Rd | 140 ++++----- man/levene_test.Rd | 42 +- man/mean_n.Rd | 138 ++++---- man/mn.Rd |only man/mwu.Rd | 104 +++--- man/nhanes_sample.Rd | 30 - man/odds_to_rr.Rd | 138 ++++---- man/overdisp.Rd | 146 ++++----- man/pred_accuracy.Rd | 112 +++---- man/pred_vars.Rd | 76 ++-- man/prop.Rd | 188 +++++++----- man/r2.Rd | 240 +++++++-------- man/re_var.Rd | 124 ++++---- man/reliab_test.Rd | 312 ++++++++++---------- man/rmse.Rd | 152 ++++----- man/robust.Rd | 164 +++++----- man/se.Rd | 270 ++++++++--------- man/se_ybar.Rd | 58 +-- man/smpsize_lmm.Rd | 128 ++++---- man/std_beta.Rd | 136 ++++---- man/svyglm.nb.Rd | 129 ++++---- man/table_values.Rd | 72 ++-- man/var_pop.Rd | 78 ++--- man/weight.Rd | 114 +++---- man/wtd_sd.Rd | 66 ++-- man/xtab_statistics.Rd | 220 +++++++------- 59 files changed, 3959 insertions(+), 3632 deletions(-)
Title: Accesses Air Quality Data from the Open Data Platform OpenAQ
Description: Allows access to air quality data from the API of the OpenAQ
platform <https://docs.openaq.org/>, with the different services the API offers
(getting measurements for a given query, getting latest measurements, getting
lists of available countries/cities/locations).
Author: Maëlle Salmon [aut, cre],
Andrew MacDonald [ctb] (Andrew MacDonald reviewed the package for
rOpenSci, see https://github.com/ropensci/onboarding/issues/24),
Andy Teucher [ctb] (Andy Teucher reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/24),
Mikayla Murphy [ctb]
Maintainer: Maëlle Salmon <maelle.salmon@yahoo.se>
Diff between ropenaq versions 0.1.3 dated 2016-09-14 and 0.1.4 dated 2017-04-11
ropenaq-0.1.3/ropenaq/inst/doc/animated-map.R |only ropenaq-0.1.3/ropenaq/inst/doc/animated-map.Rmd |only ropenaq-0.1.3/ropenaq/inst/doc/animated-map.html |only ropenaq-0.1.3/ropenaq/vignettes/animated-map.Rmd |only ropenaq-0.1.4/ropenaq/DESCRIPTION | 28 ropenaq-0.1.4/ropenaq/MD5 | 79 - ropenaq-0.1.4/ropenaq/NAMESPACE | 2 ropenaq-0.1.4/ropenaq/NEWS.md | 12 ropenaq-0.1.4/ropenaq/R/cities.R | 13 ropenaq-0.1.4/ropenaq/R/countries.R | 11 ropenaq-0.1.4/ropenaq/R/latest.R | 7 ropenaq-0.1.4/ropenaq/R/locations.R | 15 ropenaq-0.1.4/ropenaq/R/measurements.R | 7 ropenaq-0.1.4/ropenaq/R/utils.R | 228 ++- ropenaq-0.1.4/ropenaq/build/vignette.rds |binary ropenaq-0.1.4/ropenaq/inst/doc/Ropenaq-vignette.R | 54 ropenaq-0.1.4/ropenaq/inst/doc/Ropenaq-vignette.Rmd | 33 ropenaq-0.1.4/ropenaq/inst/doc/Ropenaq-vignette.html | 740 ---------- ropenaq-0.1.4/ropenaq/inst/doc/graphics_of_pm_25_concentrations_in_several_countries.R | 45 ropenaq-0.1.4/ropenaq/inst/doc/graphics_of_pm_25_concentrations_in_several_countries.Rmd | 13 ropenaq-0.1.4/ropenaq/inst/doc/graphics_of_pm_25_concentrations_in_several_countries.html | 15 ropenaq-0.1.4/ropenaq/inst/doc/mapping_openaq_monitors.R | 46 ropenaq-0.1.4/ropenaq/inst/doc/mapping_openaq_monitors.Rmd | 13 ropenaq-0.1.4/ropenaq/inst/doc/mapping_openaq_monitors.html | 22 ropenaq-0.1.4/ropenaq/inst/doc/using_openair_package_with_openaq_data.R | 50 ropenaq-0.1.4/ropenaq/inst/doc/using_openair_package_with_openaq_data.Rmd | 55 ropenaq-0.1.4/ropenaq/inst/doc/using_openair_package_with_openaq_data.html | 52 ropenaq-0.1.4/ropenaq/man/aq_cities.Rd | 11 ropenaq-0.1.4/ropenaq/man/aq_countries.Rd | 9 ropenaq-0.1.4/ropenaq/man/aq_latest.Rd | 7 ropenaq-0.1.4/ropenaq/man/aq_locations.Rd | 15 ropenaq-0.1.4/ropenaq/man/aq_measurements.Rd | 7 ropenaq-0.1.4/ropenaq/tests/testthat/test-async.R |only ropenaq-0.1.4/ropenaq/tests/testthat/test-buildQueries.R | 45 ropenaq-0.1.4/ropenaq/tests/testthat/test-cities.R | 5 ropenaq-0.1.4/ropenaq/tests/testthat/test-countries.R | 1 ropenaq-0.1.4/ropenaq/tests/testthat/test-latest.R | 10 ropenaq-0.1.4/ropenaq/tests/testthat/test-locations.R | 5 ropenaq-0.1.4/ropenaq/tests/testthat/test-measurements.R | 19 ropenaq-0.1.4/ropenaq/vignettes/Ropenaq-vignette.Rmd | 33 ropenaq-0.1.4/ropenaq/vignettes/graphics_of_pm_25_concentrations_in_several_countries.Rmd | 13 ropenaq-0.1.4/ropenaq/vignettes/mapping_openaq_monitors.Rmd | 13 ropenaq-0.1.4/ropenaq/vignettes/using_openair_package_with_openaq_data.Rmd | 55 43 files changed, 408 insertions(+), 1380 deletions(-)
Title: Fast and Simple 'MongoDB' Client for R
Description: High-performance 'MongoDB' client based on 'libmongoc' and 'jsonlite'.
Includes support for aggregation, indexing, map-reduce, streaming, encryption,
enterprise authentication. The online user manual provides an overview of the
available methods in the package: <https://jeroen.github.io/mongolite/>.
Author: Jeroen Ooms [aut, cre],
MongoDB, Inc [cph] (Author of mongo-c-driver)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between mongolite versions 1.1 dated 2017-03-18 and 1.2 dated 2017-04-11
DESCRIPTION | 12 +++++++----- MD5 | 22 +++++++++++----------- NAMESPACE | 1 + NEWS | 5 +++++ R/options.R | 13 ++++++++++--- man/mongo_options.Rd | 5 ++++- src/bson.c | 23 +++++++++++++++++++++-- src/bson/bson-version.h | 6 +++--- src/mongoc/mongoc-config.h | 2 ++ src/mongoc/mongoc-socket.c | 15 ++++++++++----- src/mongoc/mongoc-socket.h | 6 +----- src/mongoc/mongoc-version.h | 6 +++--- 12 files changed, 78 insertions(+), 38 deletions(-)
Title: Evaluation of Classification Model Options
Description: Designed to assist novice to intermediate analysts in choosing
an optimal classification model, particularly for working with relatively
small data sets. It provides cross-validated results comparing several
different models at once using a consistent set of performance metrics,
so users can hone in on the most promising approach rather than attempting
single model fittings at a time. The package predefined 12 most common
classification models, although users are free to select from the 200+
other options available in caret package.
Author: Younggun You [cre],
Eric Stickney [aut]
Maintainer: Younggun You <younggun@stanford.edu>
Diff between modeval versions 0.1.2 dated 2017-03-29 and 0.1.3 dated 2017-04-11
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/code.R | 47 ++--------------------------------------------- inst/doc/modeval.html | 42 +++++++++++++++++++++--------------------- 4 files changed, 29 insertions(+), 72 deletions(-)
Title: JSON for Linking Data
Description: JSON-LD is a light-weight syntax for expressing linked data. It is primarily
intended for web-based programming environments, interoperable web services and for
storing linked data in JSON-based databases. This package provides bindings to the
JavaScript library for converting, expanding and compacting JSON-LD documents.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between jsonld versions 1.1 dated 2016-12-16 and 1.2 dated 2017-04-11
DESCRIPTION | 12 LICENSE | 2 MD5 | 10 NEWS | 3 R/wrappers.R | 10 inst/js/jsonld.js | 2534 ++++++++++++++++++++++++++++++++++++------------------ 6 files changed, 1749 insertions(+), 822 deletions(-)
More information about FactoInvestigate at CRAN
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